Patent Publication Number: US-2022228219-A1

Title: Target-enriched multiplexed parallel analysis for assessment of tumor biomarkers

Description:
CROSS REFERENCE TO RELATED PATENT APPLICATIONS 
     This application is a U.S. national phase application of International Application No. PCT/EP2018/068441, which was filed on Jul. 6, 2018, and claims priority to U.S. Provisional Application No. 62/529,779, which was filed on Jul. 7, 2017. The content of these earlier filed applications is hereby incorporated by reference herein in its entirety. 
    
    
     INCORPORATION OF THE SEQUENCE LISTING 
     The present application contains a sequence listing that was submitted herewith in ASCII format via EFS-Web, containing the file name “37578_0073U1_SL” which is 389,120 bytes in size, created on Dec. 18, 2019, and is herein incorporated by reference in its entirety pursuant to 37 C.F.R. § 1.52(e)(5). 
     FIELD OF THE INVENTION 
     The invention is in the field of biology, medicine and chemistry, more in particular in the field of molecular biology and more in particular in the field of molecular diagnostics. 
     BACKGROUND OF THE INVENTION 
     The identification of tumor biomarkers has been an important advance in the detection, diagnosis and treatment of a wide variety of cancers. Various methods of detecting tumor biomarkers are known in the art; however, additional methods are still needed, in particular methods that allow for detection of tumor biomarkers non-invasively, such as in a plasma sample (liquid biopsy). The identification of hereditary (germline) mutations in patients with cancer or high risk individuals suspected of cancer-predisposing syndrome is a useful clinical tool that enables early medical intervention, prophylactic surgery and close monitoring. These germline mutations can be identified in an individual&#39;s healthy tissue (such as buccal swab or lymphocytes). 
     Next generation sequencing (NGS) technologies have been implemented in the development of non-invasive prenatal testing (NIPT). In 2008, two independent groups demonstrated that NIPT of trisomy 21 could be achieved using next generation massively parallel shotgun sequencing (MPSS) (Chiu, R. W. et al.(2008)  Proc. Natl. Acad. Sci. USA  105:20458-20463; Fan, H. C. et al.(2008)  Proc. Natl. Acad. Sci. USA  105:16266-162710). Large-scale clinical studies using NGS for NIPT have been described (Palomaki, G. E. et al. (2011) Genet. Med. 13:913-920; Ehrich, M. et al. (2011)  Am. J. Obstet. Gynecol.  204:205e1-11; Chen, E. Z. et al. (2011)  PLoS One  6:e21791; Sehnert, A. J. et al. (2011)  Clin. Chem.  57:1042-1049; Palomaki, G. E. et al. (2012);  Genet. Med.  14:296-305; Bianchi, D. W. et al. (2012)  Obstet. Gynecol.  119:890-901; Zimmerman, B. et al. (2012)  Prenat. Diag.  32:1233-1241; Nicolaides, K. H. et al. (2013)  Prenat. Diagn.  33:575-579; Sparks, A. B. et al. (2012)  Prenat. Diagn.  32:3-9). 
     Initial NIPT approaches used massively parallel shotgun sequencing (MPSS) NGS methodologies (see e.g., U.S. Pat. Nos. 7,888,017; 8,008,018; 8,195,415; 8,296,076; 8,682,594; US Patent Publication 20110201507; US Patent Publication 20120270739). Thus, these approaches are whole genome-based. More recently, targeted-based NGS approaches for NIPT, in which only specific sequences of interest are sequenced, have been developed. For example, a targeted NIPT approach using TArget Capture Sequences (TACS) for identifying fetal chromosomal abnormalities using a maternal blood sample has been described (PCT Publication WO 2016/189388; US Patent Publication 2016/0340733; Koumbaris, G. et al. (2016)  Clinical chemistry,  62(6), pp.848-855.). Such targeted approaches require significantly less sequencing than the MPSS approaches, since sequencing is only performed on specific loci on the target sequence of interest rather than across the whole genome. 
     Additional methodologies for NGS-based approaches are still needed, in particular approaches that can target specific sequences of interest, such as for example tumor biomarkers, thereby greatly reducing the amount of sequencing needed as compared to whole genome-based approaches, as well as increasing the read-depth of regions of interest, thus enabling detection of low signal to noise ratio regions. In particular, additional methodologies are still needed that allow for genetic aberrations present in diminutive amounts in a sample to be reliably detected, such as for example in the early detection of cancer. 
     SUMMARY OF THE INVENTION 
     This invention provides improved methods for enriching targeted genomic regions of interest to be analyzed by multiplexed parallel sequencing, wherein the enriched sequences are tumor biomarker sequences and the DNA sample used in the method is from a subject having or suspected of having a tumor. Accordingly, the methods allow for detection of tumor biomarkers in a variety of biological samples, including liquid samples, such as plasma samples (liquid biopsy), thereby providing non-invasive means for tumor detection and monitoring. The methods of the invention utilize a pool of TArget Capture Sequences (TACS) designed such that the sequences within the pool have features that optimize the efficiency, specificity and accuracy of genetic assessment of tumor biomarkers. The methods of the invention can be used, for example, in cancer diagnosis, cancer screening, cancer treatment regimen selection and/or cancer therapy monitoring. 
     Accordingly, in one aspect, the invention pertains to a method of detecting one or more tumor biomarkers in a DNA sample from a subject having or suspected of having a tumor, the method comprising: 
     (a) preparing a sequencing library from the DNA sample; 
     (b) hybridizing the sequencing library to a pool of double-stranded TArget Capture Sequences (TACS) that bind to one or more tumor biomarker sequences of interest, wherein:
         (i) each member sequence within the pool of TACS is between 100-500 base pairs in length, each member sequence having a 5′ end and a 3′ end;   (ii) preferably each member sequence binds to the tumor biomarker sequence of interest at least 50 base pairs away, on both the 5′ end and the 3′ end, from regions harboring Copy Number Variations (CNVs), Segmental duplications or repetitive DNA elements; and   (iii) the GC content of the pool of TACS is between 19% and 80%, as determined by calculating the GC content of each member within the pool of TACS;       

     (c) isolating members of the sequencing library that bind to the pool of TACS to obtain an enriched library; 
     (d) amplifying and sequencing the enriched library; and 
     (e) performing statistical analysis on the enriched library sequences, optionally utilizing only fragments of a specific size range, to thereby detect the tumor biomarker(s) in the DNA sample. 
     In one embodiment, the pool of TACS comprises a plurality of TACS families, wherein each member of a TACS family binds to the same tumor biomarker sequence of interest but with different start and/or stop positions on the sequence with respect to a reference coordinate system (i.e., binding of TACS family members to the target sequence is staggered) to thereby enrich for target sequences of interest, followed by massive parallel sequencing and statistical analysis of the enriched population. The use of families of TACS with the TACS pool that bind to each target sequence of interest, as compared to use of a single TACS within the TACS pool that binds to each target sequence of interest, significantly increases enrichment for the target sequences of interest, as evidenced by a greater than 50% average increase in read-depth for the family of TACS versus a single TACS. Herein, the mutations detected or biomarkers detected may be due to somatic mutation or may be hereditary, i.e already present in the germ line. 
     Accordingly, in one embodiment, the pool of TACS comprises a plurality of TACS families directed to different tumor biomarker sequences of interest, wherein each TACS family comprises a plurality of member sequences, wherein each member sequence binds to the same tumor biomarker sequence of interest but has different start and/or stop positions with respect to a reference coordinate system for the genomic sequence of interest. 
     In certain embodiments, each TACS family comprises at least 3 member sequences or at least 5 member sequences. Alternative numbers of member sequences in each TACS family are described herein. In one embodiment, the pool of TACS comprises at least 50 different TACS families. Alternative numbers of different TACS families within the pool of TACS are described herein. In certain embodiments, the start and/or stop positions for the member sequences within a TACS family, with respect to a reference coordinate system for the genomic sequence of interest, are staggered by at least 3 base pairs or at least 5 base pairs or by at least 10 base pairs. Alternative lengths (sizes) for the number of base pairs within the stagger are described herein. 
     In one embodiment, each member sequence within the pool of TACS is at least 160 base pairs in length. In certain embodiments, the GC content of the pool of TACS is between 19% and 80% or is between 19% and 46%. Alternative % ranges for the GC content of the pool of TACS are described herein. 
     In one embodiment, the pool of TACS is fixed to a solid support. For example, in one embodiment, the TACS are biotinylated and are bound to streptavidin-coated magnetic beads. 
     In one embodiment, amplification of the enriched library is performed in the presence of blocking sequences that inhibit amplification of wild-type sequences. 
     In one embodiment, members of the sequencing library that bind to the pool of TACS are partially complementary to the TACS. 
     In one embodiment, the statistical analysis comprises a segmentation algorithm, for example, likelihood-based segmentation, segmentation using small overlapping windows, segmentation using parallel pairwise testing, and combinations thereof. In one embodiment, the statistical analysis comprises a score-based classification system. In one embodiment, sequencing of the enriched library provides a read-depth for the genomic sequences of interest and read-depths for reference loci and the statistical analysis comprises applying an algorithm that tests sequentially the read-depth of the loci of from the genomic sequences of interest against the read-depth of the reference loci, the algorithm comprising steps for: (a) removal of inadequately sequenced loci; (b) GC-content bias alleviation; and (c) genetic status determination. In one embodiment, GC-content bias is alleviated by grouping together loci of matching GC content. In one embodiment, sequencing of the enriched library provides the number and size of sequenced fragments for TACS-specific coordinates and the statistical analysis comprises applying an algorithm that tests sequentially the fragment-size proportion for the genomic sequence of interest against the fragment-size proportion of the reference loci, the algorithm comprising steps for: (a) removal of fragment-size outliers; (b) fragment-size proportion calculation; and (c) genetic status determination. 
     In one embodiment, the DNA sample comprises cell free tumor DNA (cftDNA). In various embodiments, the DNA sample is selected from a group comprising of a plasma sample, a urine sample, a sputum sample, a cerebrospinal fluid sample, an ascites sample and a pleural effusion sample from subject having or suspected of having a tumor. In one embodiment, the DNA sample is from a tissue sample from a subject having or suspected of having a tumor. 
     In one embodiment, the pool of TACS binds to a plurality of tumor biomarker sequences of interest selected from a group comprising ABL, AKT, AKT1, ALK, APC, AR, ARAF, ATM, BAP1, BARD1, BCL, BMPR1A, BRAF, BRCA, BRCA1, BRCA2, BRIP1, CDH1, CDKN, CHEK2, CTNNB1, DDB2, DDR2, DICER1, EGFR, EPCAM, ErbB, ErcC, ESR1, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FBXW7, FGFR, FLT, FLT3, FOXA1, FOXL2, GATA3, GNA11, GNAQ, GNAS, GREM1, HOX, HOXB13, HRAS, IDH1, JAK, JAK2, KEAP1, KIT, KRAS, MAP2Ks, MAP3Ks, MET, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, NBN, NPM1, NRAS, NTRK1, PALB2, PDGFRs, PI3KCs, PMS2, POLD1, POLE, POLH, PTEN, RAD50, RAD51C, RAD51D, RAF1, RB1, RET, RUNX1, SLX4, SMAD, SMAD4, SMARCA4, SPOP, STAT, STK11, TP53, VHL, XPA and XPC, and combinations thereof. 
     In another embodiment, the pool of TACS binds to a plurality of tumor biomarker sequences of interest selected from a group comprising, AKT1, ALK, APC, AR, ARAF, ATM, BAP1, BARD1, BMPR1A, BRAF, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDKN2A (p14ARF), CDKN2A (p16INK4a), CHEK2, CTNNB1, DDB2, DDR2, DICER1, EGFR, EPCAM, ERBB2, ERBB3, ERBB4, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ESR1, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FBXW7, FGFR1, FGFR2, FLT3, FOXA1, FOXL2, GATA3, GNA11, GNAQ, GNAS, GREM1, HOXB13, IDH1, IDH2, JAK2, KEAP1, KIT, KRAS, MAP2K1, MAP3K1, MEN1, MET, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, MYC, MYCN, NBN, NPM1, NRAS, NTRK1, PALB2, PDGFRA, PIK3CA, PIK3CB, PMS2, POLD1, POLE, POLH, PTEN, RAD50, RAD51C, RAD51D, RAF1, RB1, RET, ROS1, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SLX4, SMAD4, SMARCA4, SPOP, STAT, STK11, TMPRSS2, TP53, VHL, XPA, XPC and combinations thereof. 
     In one embodiment, the pool of TACS binds to a plurality of tumor biomarker sequences of interest selected from a group comprising EGFR_6240, KRAS_521, EGFR_6225, NRAS_578, NRAS_580, PIK3CA_763, EGFR_13553, EGFR_18430, BRAF_476, KIT_1314, NRAS_584, EGFR_12378, and combinations thereof. 
     In another embodiment, the pool of TACS binds to a plurality of tumor biomarker sequences of interest selected from a group comprising COSM6240 (EGFR_6240), COSM521 (KRAS_521), COSM6225 (EGFR_6225), COSM578 (NRAS_578), COSM580 (NRAS_580), COSM763 (PIK3CA_763), COSM13553 (EGFR_13553), COSM18430 (EGFR_18430), COSM476 (BRAF_476), COSM1314 (KIT_1314), COSM584 (NRAS_584), COSM12378 (EGFR_12378), and combinations thereof, wherein the identifiers refer to the COSMIC database ID number of the biomarker. 
     In one embodiment, the method further comprises making a diagnosis of the subject based on detection of at least one tumor biomarker sequence. In another embodiment, the method further comprises selecting a therapeutic regimen for the subject based on detection of at least one tumor biomarker sequence. In yet another embodiment, the method further comprises monitoring treatment efficacy of a therapeutic regimen in the subject based on detection of at least one tumor biomarker sequence. 
     In another aspect, kits for performing the methods of the invention are also encompassed. 
    
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
       The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. 
         FIG. 1  is a schematic diagram of multiplexed parallel analysis of targeted genomic regions for non-invasive prenatal testing using TArget Capture Sequences (TACS). 
         FIG. 2  is a listing of exemplary chromosomal regions for amplifying TACS that bind to for example chromosomes 13, 18, 21 or X. A more extensive list is shown in Table 1 below. 
         FIG. 3  is a schematic diagram of TACS-based enrichment of a sequence of interest (bold line) using a single TACS (left) versus TACS-based enrichment using a family of TACS (right). 
         FIGS. 4A-4B  are graphs showing enrichment using families of TACS versus a single TACS, as illustrated by increase in the average read-depth.  FIG. 4A  shows loci enriched using a family of TACS (red dots) as compared to loci enriched using a single TACS (blue dots), with different target sequences shown on the x-axis and the fold change in read-depth shown on the y-axis.  FIG. 4B  is a bar graph illustrating the average fold-increase in read-depth (54.7%) using a family of TACS (right) versus a single TACS (left). 
         FIG. 5  shows bar graphs illustrating detection of known genetic mutations that are tumor biomarkers in certified reference material harboring the mutations. Two replicates of the reference material are shown. The line illustrates the expected minor allele frequency (MAF) for each of the assessed tumor loads. The bars (x-axis) illustrate the detected MAF (y-axis) for the indicated genetic mutations in the certified reference material. 
         FIG. 6  shows bar graphs illustrating detection of tumor biomarkers in cancer patient samples. Results are shown for two patients, one harboring mutation PIK3CA E545K (top bars) and one harboring mutation TP53 K139 (bottom bars). Both tumor tissue samples (“Tissue Rep. 1” and “Tissue Rep. 2”) and plasma samples (“Plasma”) are shown. The y-axis shows % variant allele frequency (VAF) detected in the samples. 
         FIG. 7  is a bar graph showing the observed pattern of somatic SNVs in breast cancer, as found in the COSMIC database. The x-axis shows a single base mutation observed in cancer in the context of its neighboring sequences. For example A[C&gt;A]T describes the mutation of Cytosine (C) to Adenine (A) where the upstream sequence is Adenine and the downstream sequence is Thymine. The y-axis shows the frequency of occurrence of this mutation in breast cancer. 
         FIG. 8  is a bar graph showing results of a simulations study where simulated sequencing data includes mutational motifs. The data were subjected to mutational motif detection. The bars indicate the average estimated frequency of the known mutational breast cancer motifs computed from a data set of 10000 simulations. Results illustrate that detection of mutational motifs is possible using the developed algorithm. 
         FIG. 9  is a dot plot graph showing results of a fragments-based test for detecting increased numbers of smaller-size fragments in a mixed sample. An abnormal, aneuploid sample, with an estimated fetal fraction of 2.8%, was correctly detected using this method. The black dots are individual samples. The x-axis shows the sample index. The y-axis shows the score result of the fragments-size based method. A score result greater than the threshold shown by the grey line indicates a deviation from the expected size of fragments illustrating the presence of aneuploidy. 
         FIG. 10  is a listing of exemplary chromosomal regions for amplifying TACS that bind to exemplary, non-limiting tumor biomarker genes. 
       Table 1 shows exemplary and preferred TACS positions. 
       
         
           
             
                 
                 
                 
                 
                 
                 
               
                 
                     
                     
                 
                 
                     
                   Chr. 
                   Start 
                   Stop 
                   GC 
                   Gene 
                 
                 
                     
                     
                 
               
              
                 
                     
                 
              
             
             
                 
                 
                 
                 
                 
                 
              
                 
                     
                   chr1 
                   11169250 
                   11169491 
                   0.434 
                   MTOR 
                 
                 
                     
                   chr1 
                   11169262 
                   11169509 
                   0.419 
                   MTOR 
                 
                 
                     
                   chr1 
                   11169280 
                   11169519 
                   0.400 
                   MTOR 
                 
                 
                     
                   chr1 
                   11169299 
                   11169548 
                   0.392 
                   MTOR 
                 
                 
                     
                   chr1 
                   11174376 
                   11174632 
                   0.541 
                   MTOR 
                 
                 
                     
                   chr1 
                   11174392 
                   11174632 
                   0.535 
                   MTOR 
                 
                 
                     
                   chr1 
                   11174392 
                   11174691 
                   0.527 
                   MTOR 
                 
                 
                     
                   chr1 
                   11174468 
                   11174698 
                   0.515 
                   MTOR 
                 
                 
                     
                   chr1 
                   11184541 
                   11184796 
                   0.504 
                   MTOR 
                 
                 
                     
                   chr1 
                   11184563 
                   11184812 
                   0.504 
                   MTOR 
                 
                 
                     
                   chr1 
                   11184564 
                   11184816 
                   0.502 
                   MTOR 
                 
                 
                     
                   chr1 
                   11187992 
                   11188236 
                   0.535 
                   MTOR 
                 
                 
                     
                   chr1 
                   11188010 
                   11188249 
                   0.521 
                   MTOR 
                 
                 
                     
                   chr1 
                   11188018 
                   11188257 
                   0.513 
                   MTOR 
                 
                 
                     
                   chr1 
                   11188029 
                   11188274 
                   0.492 
                   MTOR 
                 
                 
                     
                   chr1 
                   17345194 
                   17345459 
                   0.316 
                   SDHB 
                 
                 
                     
                   chr1 
                   17349096 
                   17349342 
                   0.543 
                   SDHB 
                 
                 
                     
                   chr1 
                   17350413 
                   17350563 
                   0.497 
                   SDHB 
                 
                 
                     
                   chr1 
                   17350566 
                   17350779 
                   0.430 
                   SDHB 
                 
                 
                     
                   chr1 
                   17354089 
                   17354304 
                   0.463 
                   SDHB 
                 
                 
                     
                   chr1 
                   17355058 
                   17355208 
                   0.417 
                   SDHB 
                 
                 
                     
                   chr1 
                   17359477 
                   17359689 
                   0.427 
                   SDHB 
                 
                 
                     
                   chr1 
                   17371214 
                   17371394 
                   0.470 
                   SDHB 
                 
                 
                     
                   chr1 
                   17380408 
                   17380619 
                   0.670 
                   SDHB 
                 
                 
                     
                   chr1 
                   43814917 
                   43815186 
                   0.633 
                   MPL 
                 
                 
                     
                   chr1 
                   45795001 
                   45795250 
                   0.536 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45796024 
                   45796223 
                   0.530 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45796871 
                   45797092 
                   0.536 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45797060 
                   45797289 
                   0.648 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45797289 
                   45797529 
                   0.635 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45797602 
                   45797802 
                   0.577 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45797819 
                   45798019 
                   0.622 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45797986 
                   45798270 
                   0.593 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45798204 
                   45798404 
                   0.602 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45798364 
                   45798564 
                   0.547 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45798532 
                   45798732 
                   0.557 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45798672 
                   45798872 
                   0.567 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45798867 
                   45799097 
                   0.628 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45799150 
                   45799357 
                   0.582 
                   MUTYH 
                 
                 
                     
                   chr1 
                   45800062 
                   45800304 
                   0.539 
                   MUTYH 
                 
                 
                     
                   chr1 
                   115252133 
                   115252352 
                   0.445 
                   NRAS 
                 
                 
                     
                   chr1 
                   115252133 
                   115252354 
                   0.441 
                   NRAS 
                 
                 
                     
                   chr1 
                   115252138 
                   115252350 
                   0.446 
                   NRAS 
                 
                 
                     
                   chr1 
                   115252142 
                   115252350 
                   0.450 
                   NRAS 
                 
                 
                     
                   chr1 
                   115256347 
                   115256588 
                   0.409 
                   NRAS 
                 
                 
                     
                   chr1 
                   115256398 
                   115256647 
                   0.448 
                   NRAS 
                 
                 
                     
                   chr1 
                   115256410 
                   115256649 
                   0.458 
                   NRAS 
                 
                 
                     
                   chr1 
                   115256442 
                   115256691 
                   0.440 
                   NRAS 
                 
                 
                     
                   chr1 
                   115256467 
                   115256726 
                   0.442 
                   NRAS 
                 
                 
                     
                   chr1 
                   115256470 
                   115256715 
                   0.451 
                   NRAS 
                 
                 
                     
                   chr1 
                   115258538 
                   115258778 
                   0.440 
                   NRAS 
                 
                 
                     
                   chr1 
                   115258570 
                   115258813 
                   0.463 
                   NRAS 
                 
                 
                     
                   chr1 
                   115258607 
                   115258846 
                   0.492 
                   NRAS 
                 
                 
                     
                   chr1 
                   115258659 
                   115258901 
                   0.444 
                   NRAS 
                 
                 
                     
                   chr1 
                   156268500 
                   156268651 
                   0.454 
                   VHLL 
                 
                 
                     
                   chr1 
                   156269007 
                   156269221 
                   0.493 
                   VHLL 
                 
                 
                     
                   chr1 
                   156846129 
                   156846362 
                   0.641 
                   NTRK1 
                 
                 
                     
                   chr1 
                   156846129 
                   156846377 
                   0.643 
                   NTRK1 
                 
                 
                     
                   chr1 
                   156846130 
                   156846362 
                   0.639 
                   NTRK1 
                 
                 
                     
                   chr1 
                   156848889 
                   156849132 
                   0.611 
                   NTRK1 
                 
                 
                     
                   chr1 
                   156848911 
                   156849153 
                   0.617 
                   NTRK1 
                 
                 
                     
                   chr1 
                   156848921 
                   156849168 
                   0.613 
                   NTRK1 
                 
                 
                     
                   chr1 
                   156848925 
                   156849168 
                   0.611 
                   NTRK1 
                 
                 
                     
                   chr1 
                   161284168 
                   161284376 
                   0.598 
                   SDHC 
                 
                 
                     
                   chr1 
                   161293229 
                   161293429 
                   0.343 
                   SDHC 
                 
                 
                     
                   chr1 
                   161298181 
                   161298414 
                   0.436 
                   SDHC 
                 
                 
                     
                   chr1 
                   161333007 
                   161333261 
                   0.447 
                   SDHC 
                 
                 
                     
                   chr1 
                   161333275 
                   161333550 
                   0.391 
                   SDHC 
                 
                 
                     
                   chr1 
                   161333589 
                   161333868 
                   0.439 
                   SDHC 
                 
                 
                     
                   chr1 
                   161333890 
                   161334157 
                   0.392 
                   SDHC 
                 
                 
                     
                   chr1 
                   161334206 
                   161334492 
                   0.394 
                   SDHC 
                 
                 
                     
                   chr1 
                   162748235 
                   162748450 
                   0.440 
                   DDR2 
                 
                 
                     
                   chr1 
                   162748273 
                   162748512 
                   0.442 
                   DDR2 
                 
                 
                     
                   chr1 
                   162748316 
                   162748557 
                   0.450 
                   DDR2 
                 
                 
                     
                   chr1 
                   162748370 
                   162748580 
                   0.483 
                   DDR2 
                 
                 
                     
                   chr10 
                   8111358 
                   8111588 
                   0.506 
                   GATA3 
                 
                 
                     
                   chr10 
                   8111468 
                   8111707 
                   0.529 
                   GATA3 
                 
                 
                     
                   chr10 
                   8115737 
                   8115986 
                   0.572 
                   GATA3 
                 
                 
                     
                   chr10 
                   8115741 
                   8115988 
                   0.569 
                   GATA3 
                 
                 
                     
                   chr10 
                   8115783 
                   8115988 
                   0.612 
                   GATA3 
                 
                 
                     
                   chr10 
                   8115789 
                   8115988 
                   0.620 
                   GATA3 
                 
                 
                     
                   chr10 
                   43595933 
                   43596179 
                   0.623 
                   RET 
                 
                 
                     
                   chr10 
                   43597765 
                   43598054 
                   0.614 
                   RET 
                 
                 
                     
                   chr10 
                   43600476 
                   43600682 
                   0.686 
                   RET 
                 
                 
                     
                   chr10 
                   43601846 
                   43602088 
                   0.638 
                   RET 
                 
                 
                     
                   chr10 
                   43604444 
                   43604706 
                   0.620 
                   RET 
                 
                 
                     
                   chr10 
                   43606653 
                   43606911 
                   0.595 
                   RET 
                 
                 
                     
                   chr10 
                   43607465 
                   43607728 
                   0.659 
                   RET 
                 
                 
                     
                   chr10 
                   43608226 
                   43608455 
                   0.596 
                   RET 
                 
                 
                     
                   chr10 
                   43608980 
                   43609217 
                   0.626 
                   RET 
                 
                 
                     
                   chr10 
                   43609917 
                   43610183 
                   0.625 
                   RET 
                 
                 
                     
                   chr10 
                   43611943 
                   43612187 
                   0.522 
                   RET 
                 
                 
                     
                   chr10 
                   43613689 
                   43613933 
                   0.555 
                   RET 
                 
                 
                     
                   chr10 
                   43614921 
                   43615150 
                   0.687 
                   RET 
                 
                 
                     
                   chr10 
                   43615517 
                   43615759 
                   0.568 
                   RET 
                 
                 
                     
                   chr10 
                   43617287 
                   43617531 
                   0.457 
                   RET 
                 
                 
                     
                   chr10 
                   43619092 
                   43619322 
                   0.584 
                   RET 
                 
                 
                     
                   chr10 
                   43620303 
                   43620509 
                   0.551 
                   RET 
                 
                 
                     
                   chr10 
                   43623746 
                   43624029 
                   0.493 
                   RET 
                 
                 
                     
                   chr10 
                   43624152 
                   43624439 
                   0.490 
                   RET 
                 
                 
                     
                   chr10 
                   43624946 
                   43625222 
                   0.433 
                   RET 
                 
                 
                     
                   chr10 
                   50686414 
                   50686655 
                   0.368 
                   ERCC6 
                 
                 
                     
                   chr10 
                   88635669 
                   88635923 
                   0.333 
                   BMPR1A 
                 
                 
                     
                   chr10 
                   88649829 
                   88650073 
                   0.384 
                   BMPR1A 
                 
                 
                     
                   chr10 
                   88659444 
                   88659644 
                   0.368 
                   BMPR1A 
                 
                 
                     
                   chr10 
                   88677042 
                   88677242 
                   0.388 
                   BMPR1A 
                 
                 
                     
                   chr10 
                   89622844 
                   89623045 
                   0.594 
                   KLLN 
                 
                 
                     
                   chr10 
                   89624131 
                   89624370 
                   0.492 
                   PTEN 
                 
                 
                     
                   chr10 
                   89624178 
                   89624422 
                   0.465 
                   PTEN 
                 
                 
                     
                   chr10 
                   89624198 
                   89624444 
                   0.445 
                   PTEN 
                 
                 
                     
                   chr10 
                   89624214 
                   89624463 
                   0.436 
                   PTEN 
                 
                 
                     
                   chr10 
                   89685273 
                   89685522 
                   0.304 
                   PTEN 
                 
                 
                     
                   chr10 
                   89692746 
                   89692946 
                   0.398 
                   PTEN 
                 
                 
                     
                   chr10 
                   89692746 
                   89692977 
                   0.392 
                   PTEN 
                 
                 
                     
                   chr10 
                   89692746 
                   89692999 
                   0.402 
                   PTEN 
                 
                 
                     
                   chr10 
                   89692763 
                   89693015 
                   0.403 
                   PTEN 
                 
                 
                     
                   chr10 
                   89692787 
                   89692999 
                   0.413 
                   PTEN 
                 
                 
                     
                   chr10 
                   89711788 
                   89712024 
                   0.380 
                   PTEN 
                 
                 
                     
                   chr10 
                   89711798 
                   89712045 
                   0.367 
                   PTEN 
                 
                 
                     
                   chr10 
                   89711867 
                   89712069 
                   0.399 
                   PTEN 
                 
                 
                     
                   chr10 
                   89711880 
                   89712129 
                   0.348 
                   PTEN 
                 
                 
                     
                   chr10 
                   89717531 
                   89717770 
                   0.404 
                   PTEN 
                 
                 
                     
                   chr10 
                   89717558 
                   89717802 
                   0.408 
                   PTEN 
                 
                 
                     
                   chr10 
                   89717558 
                   89717831 
                   0.394 
                   PTEN 
                 
                 
                     
                   chr10 
                   89717571 
                   89717820 
                   0.400 
                   PTEN 
                 
                 
                     
                   chr10 
                   89717602 
                   89717831 
                   0.413 
                   PTEN 
                 
                 
                     
                   chr10 
                   89717603 
                   89717769 
                   0.455 
                   PTEN 
                 
                 
                     
                   chr10 
                   89717627 
                   89717872 
                   0.362 
                   PTEN 
                 
                 
                     
                   chr10 
                   89720757 
                   89720967 
                   0.336 
                   PTEN 
                 
                 
                     
                   chr10 
                   89720757 
                   89721005 
                   0.329 
                   PTEN 
                 
                 
                     
                   chr10 
                   89720767 
                   89720968 
                   0.337 
                   PTEN 
                 
                 
                     
                   chr10 
                   89720775 
                   89721018 
                   0.324 
                   PTEN 
                 
                 
                     
                   chr10 
                   89726371 
                   89726571 
                   0.289 
                   PTEN 
                 
                 
                     
                   chr10 
                   89726794 
                   89727038 
                   0.310 
                   PTEN 
                 
                 
                     
                   chr10 
                   89727021 
                   89727240 
                   0.282 
                   PTEN 
                 
                 
                     
                   chr10 
                   89727261 
                   89727519 
                   0.317 
                   PTEN 
                 
                 
                     
                   chr10 
                   89727756 
                   89727916 
                   0.404 
                   PTEN 
                 
                 
                     
                   chr10 
                   89727978 
                   89728203 
                   0.389 
                   PTEN 
                 
                 
                     
                   chr10 
                   89728310 
                   89728512 
                   0.389 
                   PTEN 
                 
                 
                     
                   chr10 
                   89729027 
                   89729257 
                   0.251 
                   PTEN 
                 
                 
                     
                   chr10 
                   89729816 
                   89729967 
                   0.336 
                   PTEN 
                 
                 
                     
                   chr10 
                   89730284 
                   89730433 
                   0.307 
                   PTEN 
                 
                 
                     
                   chr10 
                   89731453 
                   89731610 
                   0.329 
                   PTEN 
                 
                 
                     
                   chr11 
                   22644366 
                   22644570 
                   0.273 
                   FANCF 
                 
                 
                     
                   chr11 
                   22644511 
                   22644731 
                   0.344 
                   FANCF 
                 
                 
                     
                   chr11 
                   22644738 
                   22644938 
                   0.318 
                   FANCF 
                 
                 
                     
                   chr11 
                   22645645 
                   22645808 
                   0.348 
                   FANCF 
                 
                 
                     
                   chr11 
                   22645808 
                   22646060 
                   0.352 
                   FANCF 
                 
                 
                     
                   chr11 
                   22646058 
                   22646268 
                   0.322 
                   FANCF 
                 
                 
                     
                   chr11 
                   22646388 
                   22646588 
                   0.532 
                   FANCF 
                 
                 
                     
                   chr11 
                   22646657 
                   22646927 
                   0.598 
                   FANCF 
                 
                 
                     
                   chr11 
                   22646959 
                   22647229 
                   0.657 
                   FANCF 
                 
                 
                     
                   chr11 
                   22647378 
                   22647578 
                   0.478 
                   FANCF 
                 
                 
                     
                   chr11 
                   47236728 
                   47236949 
                   0.635 
                   DDB2 
                 
                 
                     
                   chr11 
                   47237804 
                   47238058 
                   0.537 
                   DDB2 
                 
                 
                     
                   chr11 
                   47238291 
                   47238491 
                   0.483 
                   DDB2 
                 
                 
                     
                   chr11 
                   47254333 
                   47254547 
                   0.470 
                   DDB2 
                 
                 
                     
                   chr11 
                   47256241 
                   47256494 
                   0.547 
                   DDB2 
                 
                 
                     
                   chr11 
                   47256782 
                   47257010 
                   0.594 
                   DDB2 
                 
                 
                     
                   chr11 
                   47259397 
                   47259552 
                   0.468 
                   DDB2 
                 
                 
                     
                   chr11 
                   47259555 
                   47259796 
                   0.492 
                   DDB2 
                 
                 
                     
                   chr11 
                   47260567 
                   47260808 
                   0.483 
                   DDB2 
                 
                 
                     
                   chr11 
                   61197603 
                   61197830 
                   0.588 
                   SDHAF2 
                 
                 
                     
                   chr11 
                   61205114 
                   61205296 
                   0.481 
                   SDHAF2 
                 
                 
                     
                   chr11 
                   61205433 
                   61205588 
                   0.404 
                   SDHAF2 
                 
                 
                     
                   chr11 
                   61213390 
                   61213639 
                   0.488 
                   SDHAF2 
                 
                 
                     
                   chr11 
                   61213676 
                   61213931 
                   0.508 
                   SDHAF2 
                 
                 
                     
                   chr11 
                   61213967 
                   61214232 
                   0.462 
                   SDHAF2 
                 
                 
                     
                   chr11 
                   64570946 
                   64571196 
                   0.478 
                   MEN1 
                 
                 
                     
                   chr11 
                   64571178 
                   64571436 
                   0.544 
                   MEN1 
                 
                 
                     
                   chr11 
                   64571465 
                   64571704 
                   0.546 
                   MEN1 
                 
                 
                     
                   chr11 
                   64571732 
                   64571978 
                   0.567 
                   MEN1 
                 
                 
                     
                   chr11 
                   64572483 
                   64572713 
                   0.619 
                   MEN1 
                 
                 
                     
                   chr11 
                   64573013 
                   64573278 
                   0.602 
                   MEN1 
                 
                 
                     
                   chr11 
                   64573641 
                   64573871 
                   0.593 
                   MEN1 
                 
                 
                     
                   chr11 
                   64574483 
                   64574728 
                   0.602 
                   MEN1 
                 
                 
                     
                   chr11 
                   64575094 
                   64575345 
                   0.544 
                   MEN1 
                 
                 
                     
                   chr11 
                   64575352 
                   64575623 
                   0.614 
                   MEN1 
                 
                 
                     
                   chr11 
                   64577138 
                   64577410 
                   0.634 
                   MEN1 
                 
                 
                     
                   chr11 
                   64577437 
                   64577683 
                   0.700 
                   MEN1 
                 
                 
                     
                   chr11 
                   64577902 
                   64578171 
                   0.681 
                   MEN1 
                 
                 
                     
                   chr11 
                   94150558 
                   94150800 
                   0.362 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94151042 
                   94151242 
                   0.373 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94151616 
                   94151816 
                   0.537 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94151903 
                   94152103 
                   0.343 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94152190 
                   94152390 
                   0.333 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94153182 
                   94153395 
                   0.308 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94168979 
                   94169178 
                   0.335 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94170337 
                   94170576 
                   0.300 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94178876 
                   94179116 
                   0.386 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94180384 
                   94180615 
                   0.500 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94189360 
                   94189588 
                   0.323 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94192639 
                   94192838 
                   0.370 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94193992 
                   94194257 
                   0.301 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94197223 
                   94197451 
                   0.349 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94200864 
                   94201064 
                   0.363 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94203635 
                   94203874 
                   0.404 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94204708 
                   94204908 
                   0.368 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94209357 
                   94209557 
                   0.348 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94211862 
                   94212106 
                   0.359 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94212728 
                   94212928 
                   0.378 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94219015 
                   94219215 
                   0.348 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94219225 
                   94219425 
                   0.264 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94223880 
                   94224120 
                   0.344 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94223898 
                   94224142 
                   0.327 
                   MRE11A 
                 
                 
                     
                   chr11 
                   94225885 
                   94226125 
                   0.394 
                   MRE11A 
                 
                 
                     
                   chr11 
                   108093593 
                   108093813 
                   0.615 
                   ATM 
                 
                 
                     
                   chr11 
                   108093873 
                   108094073 
                   0.617 
                   ATM 
                 
                 
                     
                   chr11 
                   108098331 
                   108098581 
                   0.335 
                   ATM 
                 
                 
                     
                   chr11 
                   108098372 
                   108098572 
                   0.333 
                   ATM 
                 
                 
                     
                   chr11 
                   108098382 
                   108098631 
                   0.316 
                   ATM 
                 
                 
                     
                   chr11 
                   108098397 
                   108098626 
                   0.309 
                   ATM 
                 
                 
                     
                   chr11 
                   108098399 
                   108098628 
                   0.304 
                   ATM 
                 
                 
                     
                   chr11 
                   108099818 
                   108100062 
                   0.327 
                   ATM 
                 
                 
                     
                   chr11 
                   108106395 
                   108106596 
                   0.356 
                   ATM 
                 
                 
                     
                   chr11 
                   108114723 
                   108115004 
                   0.333 
                   ATM 
                 
                 
                     
                   chr11 
                   108114777 
                   108115004 
                   0.329 
                   ATM 
                 
                 
                     
                   chr11 
                   108115492 
                   108115736 
                   0.351 
                   ATM 
                 
                 
                     
                   chr11 
                   108117690 
                   108117930 
                   0.324 
                   ATM 
                 
                 
                     
                   chr11 
                   108119692 
                   108119907 
                   0.343 
                   ATM 
                 
                 
                     
                   chr11 
                   108119737 
                   108119952 
                   0.361 
                   ATM 
                 
                 
                     
                   chr11 
                   108121367 
                   108121602 
                   0.377 
                   ATM 
                 
                 
                     
                   chr11 
                   108121609 
                   108121764 
                   0.359 
                   ATM 
                 
                 
                     
                   chr11 
                   108122506 
                   108122706 
                   0.363 
                   ATM 
                 
                 
                     
                   chr11 
                   108122716 
                   108122936 
                   0.317 
                   ATM 
                 
                 
                     
                   chr11 
                   108123498 
                   108123718 
                   0.321 
                   ATM 
                 
                 
                     
                   chr11 
                   108124529 
                   108124729 
                   0.393 
                   ATM 
                 
                 
                     
                   chr11 
                   108126954 
                   108127154 
                   0.363 
                   ATM 
                 
                 
                     
                   chr11 
                   108128041 
                   108128241 
                   0.294 
                   ATM 
                 
                 
                     
                   chr11 
                   108129523 
                   108129756 
                   0.316 
                   ATM 
                 
                 
                     
                   chr11 
                   108137908 
                   108138102 
                   0.374 
                   ATM 
                 
                 
                     
                   chr11 
                   108139112 
                   108139322 
                   0.374 
                   ATM 
                 
                 
                     
                   chr11 
                   108139329 
                   108139529 
                   0.338 
                   ATM 
                 
                 
                     
                   chr11 
                   108141794 
                   108142040 
                   0.324 
                   ATM 
                 
                 
                     
                   chr11 
                   108142019 
                   108142263 
                   0.359 
                   ATM 
                 
                 
                     
                   chr11 
                   108143141 
                   108143341 
                   0.323 
                   ATM 
                 
                 
                     
                   chr11 
                   108143328 
                   108143577 
                   0.336 
                   ATM 
                 
                 
                     
                   chr11 
                   108150264 
                   108150498 
                   0.328 
                   ATM 
                 
                 
                     
                   chr11 
                   108151721 
                   108151951 
                   0.364 
                   ATM 
                 
                 
                     
                   chr11 
                   108153427 
                   108153675 
                   0.285 
                   ATM 
                 
                 
                     
                   chr11 
                   108153471 
                   108153632 
                   0.284 
                   ATM 
                 
                 
                     
                   chr11 
                   108153471 
                   108153677 
                   0.275 
                   ATM 
                 
                 
                     
                   chr11 
                   108153505 
                   108153680 
                   0.267 
                   ATM 
                 
                 
                     
                   chr11 
                   108153510 
                   108153680 
                   0.269 
                   ATM 
                 
                 
                     
                   chr11 
                   108154843 
                   108155094 
                   0.282 
                   ATM 
                 
                 
                     
                   chr11 
                   108154858 
                   108155070 
                   0.291 
                   ATM 
                 
                 
                     
                   chr11 
                   108154954 
                   108155155 
                   0.396 
                   ATM 
                 
                 
                     
                   chr11 
                   108154962 
                   108155211 
                   0.388 
                   ATM 
                 
                 
                     
                   chr11 
                   108157899 
                   108158161 
                   0.354 
                   ATM 
                 
                 
                     
                   chr11 
                   108158376 
                   108158580 
                   0.337 
                   ATM 
                 
                 
                     
                   chr11 
                   108159642 
                   108159842 
                   0.343 
                   ATM 
                 
                 
                     
                   chr11 
                   108160273 
                   108160473 
                   0.299 
                   ATM 
                 
                 
                     
                   chr11 
                   108163344 
                   108163589 
                   0.378 
                   ATM 
                 
                 
                     
                   chr11 
                   108164044 
                   108164225 
                   0.324 
                   ATM 
                 
                 
                     
                   chr11 
                   108164078 
                   108164281 
                   0.314 
                   ATM 
                 
                 
                     
                   chr11 
                   108165595 
                   108165795 
                   0.358 
                   ATM 
                 
                 
                     
                   chr11 
                   108167798 
                   108168039 
                   0.269 
                   ATM 
                 
                 
                     
                   chr11 
                   108167811 
                   108168065 
                   0.267 
                   ATM 
                 
                 
                     
                   chr11 
                   108170423 
                   108170622 
                   0.380 
                   ATM 
                 
                 
                     
                   chr11 
                   108172321 
                   108172561 
                   0.340 
                   ATM 
                 
                 
                     
                   chr11 
                   108173513 
                   108173723 
                   0.351 
                   ATM 
                 
                 
                     
                   chr11 
                   108173723 
                   108173923 
                   0.313 
                   ATM 
                 
                 
                     
                   chr11 
                   108175366 
                   108175566 
                   0.398 
                   ATM 
                 
                 
                     
                   chr11 
                   108178629 
                   108178814 
                   0.360 
                   ATM 
                 
                 
                     
                   chr11 
                   108179595 
                   108179834 
                   0.375 
                   ATM 
                 
                 
                     
                   chr11 
                   108180801 
                   108181050 
                   0.320 
                   ATM 
                 
                 
                     
                   chr11 
                   108180821 
                   108181050 
                   0.322 
                   ATM 
                 
                 
                     
                   chr11 
                   108180821 
                   108181066 
                   0.313 
                   ATM 
                 
                 
                     
                   chr11 
                   108180871 
                   108181071 
                   0.333 
                   ATM 
                 
                 
                     
                   chr11 
                   108183026 
                   108183226 
                   0.333 
                   ATM 
                 
                 
                     
                   chr11 
                   108186520 
                   108186768 
                   0.357 
                   ATM 
                 
                 
                     
                   chr11 
                   108186672 
                   108186911 
                   0.404 
                   ATM 
                 
                 
                     
                   chr11 
                   108188080 
                   108188262 
                   0.399 
                   ATM 
                 
                 
                     
                   chr11 
                   108190668 
                   108190878 
                   0.313 
                   ATM 
                 
                 
                     
                   chr11 
                   108191937 
                   108192186 
                   0.392 
                   ATM 
                 
                 
                     
                   chr11 
                   108195999 
                   108196199 
                   0.413 
                   ATM 
                 
                 
                     
                   chr11 
                   108196116 
                   108196316 
                   0.388 
                   ATM 
                 
                 
                     
                   chr11 
                   108196772 
                   108196944 
                   0.422 
                   ATM 
                 
                 
                     
                   chr11 
                   108198304 
                   108198504 
                   0.398 
                   ATM 
                 
                 
                     
                   chr11 
                   108199732 
                   108199932 
                   0.373 
                   ATM 
                 
                 
                     
                   chr11 
                   108200863 
                   108201105 
                   0.374 
                   ATM 
                 
                 
                     
                   chr11 
                   108201993 
                   108202237 
                   0.318 
                   ATM 
                 
                 
                     
                   chr11 
                   108202461 
                   108202678 
                   0.330 
                   ATM 
                 
                 
                     
                   chr11 
                   108202483 
                   108202676 
                   0.309 
                   ATM 
                 
                 
                     
                   chr11 
                   108202496 
                   108202676 
                   0.298 
                   ATM 
                 
                 
                     
                   chr11 
                   108202530 
                   108202730 
                   0.308 
                   ATM 
                 
                 
                     
                   chr11 
                   108203403 
                   108203613 
                   0.336 
                   ATM 
                 
                 
                     
                   chr11 
                   108203427 
                   108203679 
                   0.344 
                   ATM 
                 
                 
                     
                   chr11 
                   108203480 
                   108203724 
                   0.339 
                   ATM 
                 
                 
                     
                   chr11 
                   108203524 
                   108203768 
                   0.339 
                   ATM 
                 
                 
                     
                   chr11 
                   108203540 
                   108203784 
                   0.347 
                   ATM 
                 
                 
                     
                   chr11 
                   108204436 
                   108204676 
                   0.407 
                   ATM 
                 
                 
                     
                   chr11 
                   108205641 
                   108205841 
                   0.368 
                   ATM 
                 
                 
                     
                   chr11 
                   108206452 
                   108206651 
                   0.400 
                   ATM 
                 
                 
                     
                   chr11 
                   108213868 
                   108214068 
                   0.393 
                   ATM 
                 
                 
                     
                   chr11 
                   108216481 
                   108216700 
                   0.355 
                   ATM 
                 
                 
                     
                   chr11 
                   108217894 
                   108218094 
                   0.328 
                   ATM 
                 
                 
                     
                   chr11 
                   108224395 
                   108224595 
                   0.403 
                   ATM 
                 
                 
                     
                   chr11 
                   108225445 
                   108225655 
                   0.346 
                   ATM 
                 
                 
                     
                   chr11 
                   108235722 
                   108235932 
                   0.365 
                   ATM 
                 
                 
                     
                   chr11 
                   108235932 
                   108236132 
                   0.383 
                   ATM 
                 
                 
                     
                   chr11 
                   108235986 
                   108236232 
                   0.433 
                   ATM 
                 
                 
                     
                   chr11 
                   108236004 
                   108236249 
                   0.431 
                   ATM 
                 
                 
                     
                   chr11 
                   108236050 
                   108236290 
                   0.415 
                   ATM 
                 
                 
                     
                   chr11 
                   108236051 
                   108236251 
                   0.438 
                   ATM 
                 
                 
                     
                   chr11 
                   108236071 
                   108236273 
                   0.438 
                   ATM 
                 
                 
                     
                   chr11 
                   108238313 
                   108238513 
                   0.373 
                   ATM 
                 
                 
                     
                   chr11 
                   111957513 
                   111957759 
                   0.591 
                   SDHD 
                 
                 
                     
                   chr11 
                   111959529 
                   111959746 
                   0.486 
                   SDHD 
                 
                 
                     
                   chr11 
                   111965449 
                   111965740 
                   0.414 
                   SDHD 
                 
                 
                     
                   chr11 
                   111965464 
                   111965754 
                   0.416 
                   SDHD 
                 
                 
                     
                   chr12 
                   25378488 
                   25378688 
                   0.353 
                   KRAS 
                 
                 
                     
                   chr12 
                   25378503 
                   25378751 
                   0.341 
                   KRAS 
                 
                 
                     
                   chr12 
                   25378546 
                   25378778 
                   0.352 
                   KRAS 
                 
                 
                     
                   chr12 
                   25378554 
                   25378783 
                   0.348 
                   KRAS 
                 
                 
                     
                   chr12 
                   25380153 
                   25380359 
                   0.411 
                   KRAS 
                 
                 
                     
                   chr12 
                   25380166 
                   25380337 
                   0.407 
                   KRAS 
                 
                 
                     
                   chr12 
                   25380167 
                   25380326 
                   0.406 
                   KRAS 
                 
                 
                     
                   chr12 
                   25380167 
                   25380359 
                   0.420 
                   KRAS 
                 
                 
                     
                   chr12 
                   25398080 
                   25398329 
                   0.360 
                   KRAS 
                 
                 
                     
                   chr12 
                   25398145 
                   25398394 
                   0.348 
                   KRAS 
                 
                 
                     
                   chr12 
                   25398153 
                   25398397 
                   0.351 
                   KRAS 
                 
                 
                     
                   chr12 
                   25398159 
                   25398408 
                   0.356 
                   KRAS 
                 
                 
                     
                   chr12 
                   25398186 
                   25398433 
                   0.347 
                   KRAS 
                 
                 
                     
                   chr12 
                   56478765 
                   56478994 
                   0.552 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56478781 
                   56479029 
                   0.558 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56478784 
                   56479029 
                   0.561 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56478807 
                   56479047 
                   0.560 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56481533 
                   56481774 
                   0.541 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56481559 
                   56481798 
                   0.521 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56481594 
                   56481833 
                   0.546 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56481628 
                   56481942 
                   0.530 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56481740 
                   56481979 
                   0.517 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56481773 
                   56482020 
                   0.476 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56481807 
                   56482048 
                   0.467 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56482218 
                   56482457 
                   0.513 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56482252 
                   56482491 
                   0.496 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56482278 
                   56482521 
                   0.504 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56482331 
                   56482580 
                   0.528 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56486559 
                   56486791 
                   0.502 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56486561 
                   56486791 
                   0.502 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56486566 
                   56486813 
                   0.508 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56486569 
                   56486818 
                   0.508 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56490766 
                   56491006 
                   0.523 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56490766 
                   56491013 
                   0.520 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56490773 
                   56491013 
                   0.519 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56490777 
                   56491011 
                   0.523 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56491580 
                   56491801 
                   0.554 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56491592 
                   56491801 
                   0.557 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56491596 
                   56491799 
                   0.559 
                   ERBB3 
                 
                 
                     
                   chr12 
                   56491596 
                   56491801 
                   0.558 
                   ERBB3 
                 
                 
                     
                   chr12 
                   58141882 
                   58142151 
                   0.396 
                   CDK4 
                 
                 
                     
                   chr12 
                   58142160 
                   58142391 
                   0.474 
                   CDK4 
                 
                 
                     
                   chr12 
                   58142983 
                   58143287 
                   0.570 
                   CDK4 
                 
                 
                     
                   chr12 
                   58142985 
                   58143287 
                   0.568 
                   CDK4 
                 
                 
                     
                   chr12 
                   58144413 
                   58144686 
                   0.478 
                   CDK4 
                 
                 
                     
                   chr12 
                   58144452 
                   58144687 
                   0.479 
                   CDK4 
                 
                 
                     
                   chr12 
                   58144692 
                   58144932 
                   0.490 
                   CDK4 
                 
                 
                     
                   chr12 
                   58144696 
                   58144939 
                   0.492 
                   CDK4 
                 
                 
                     
                   chr12 
                   58144957 
                   58145214 
                   0.523 
                   CDK4 
                 
                 
                     
                   chr12 
                   58145023 
                   58145294 
                   0.515 
                   CDK4 
                 
                 
                     
                   chr12 
                   58145309 
                   58145580 
                   0.544 
                   CDK4 
                 
                 
                     
                   chr12 
                   58145326 
                   58145580 
                   0.541 
                   CDK4 
                 
                 
                     
                   chr12 
                   58145924 
                   58146140 
                   0.673 
                   CDK4 
                 
                 
                     
                   chr12 
                   133200375 
                   133200607 
                   0.541 
                   POLE 
                 
                 
                     
                   chr12 
                   133200794 
                   133201005 
                   0.604 
                   POLE 
                 
                 
                     
                   chr12 
                   133200978 
                   133201217 
                   0.608 
                   POLE 
                 
                 
                     
                   chr12 
                   133201185 
                   133201425 
                   0.610 
                   POLE 
                 
                 
                     
                   chr12 
                   133201428 
                   133201670 
                   0.654 
                   POLE 
                 
                 
                     
                   chr12 
                   133202187 
                   133202429 
                   0.621 
                   POLE 
                 
                 
                     
                   chr12 
                   133202217 
                   133202436 
                   0.605 
                   POLE 
                 
                 
                     
                   chr12 
                   133202217 
                   133202437 
                   0.606 
                   POLE 
                 
                 
                     
                   chr12 
                   133202218 
                   133202437 
                   0.605 
                   POLE 
                 
                 
                     
                   chr12 
                   133202355 
                   133202555 
                   0.622 
                   POLE 
                 
                 
                     
                   chr12 
                   133202648 
                   133202868 
                   0.606 
                   POLE 
                 
                 
                     
                   chr12 
                   133208842 
                   133209042 
                   0.517 
                   POLE 
                 
                 
                     
                   chr12 
                   133209059 
                   133209259 
                   0.577 
                   POLE 
                 
                 
                     
                   chr12 
                   133209191 
                   133209391 
                   0.647 
                   POLE 
                 
                 
                     
                   chr12 
                   133210529 
                   133210806 
                   0.590 
                   POLE 
                 
                 
                     
                   chr12 
                   133212413 
                   133212654 
                   0.488 
                   POLE 
                 
                 
                     
                   chr12 
                   133214538 
                   133214738 
                   0.557 
                   POLE 
                 
                 
                     
                   chr12 
                   133215637 
                   133215885 
                   0.582 
                   POLE 
                 
                 
                     
                   chr12 
                   133218204 
                   133218451 
                   0.597 
                   POLE 
                 
                 
                     
                   chr12 
                   133218707 
                   133218953 
                   0.579 
                   POLE 
                 
                 
                     
                   chr12 
                   133219069 
                   133219298 
                   0.574 
                   POLE 
                 
                 
                     
                   chr12 
                   133219399 
                   133219599 
                   0.617 
                   POLE 
                 
                 
                     
                   chr12 
                   133219778 
                   133220012 
                   0.591 
                   POLE 
                 
                 
                     
                   chr12 
                   133219996 
                   133220226 
                   0.606 
                   POLE 
                 
                 
                     
                   chr12 
                   133220308 
                   133220545 
                   0.571 
                   POLE 
                 
                 
                     
                   chr12 
                   133225529 
                   133225773 
                   0.612 
                   POLE 
                 
                 
                     
                   chr12 
                   133225887 
                   133226117 
                   0.645 
                   POLE 
                 
                 
                     
                   chr12 
                   133226161 
                   133226408 
                   0.613 
                   POLE 
                 
                 
                     
                   chr12 
                   133233672 
                   133233909 
                   0.550 
                   POLE 
                 
                 
                     
                   chr12 
                   133233774 
                   133234003 
                   0.557 
                   POLE 
                 
                 
                     
                   chr12 
                   133234350 
                   133234550 
                   0.458 
                   POLE 
                 
                 
                     
                   chr12 
                   133235953 
                   133236173 
                   0.534 
                   POLE 
                 
                 
                     
                   chr12 
                   133237539 
                   133237827 
                   0.543 
                   POLE 
                 
                 
                     
                   chr12 
                   133237547 
                   133237781 
                   0.519 
                   POLE 
                 
                 
                     
                   chr12 
                   133238036 
                   133238236 
                   0.468 
                   POLE 
                 
                 
                     
                   chr12 
                   133240495 
                   133240681 
                   0.545 
                   POLE 
                 
                 
                     
                   chr12 
                   133241011 
                   133241211 
                   0.587 
                   POLE 
                 
                 
                     
                   chr12 
                   133241805 
                   133242034 
                   0.600 
                   POLE 
                 
                 
                     
                   chr12 
                   133244016 
                   133244246 
                   0.563 
                   POLE 
                 
                 
                     
                   chr12 
                   133244860 
                   133245070 
                   0.578 
                   POLE 
                 
                 
                     
                   chr12 
                   133245148 
                   133245397 
                   0.616 
                   POLE 
                 
                 
                     
                   chr12 
                   133245378 
                   133245623 
                   0.537 
                   POLE 
                 
                 
                     
                   chr12 
                   133248734 
                   133248981 
                   0.556 
                   POLE 
                 
                 
                     
                   chr12 
                   133249169 
                   133249404 
                   0.568 
                   POLE 
                 
                 
                     
                   chr12 
                   133249662 
                   133249902 
                   0.539 
                   POLE 
                 
                 
                     
                   chr12 
                   133250240 
                   133250445 
                   0.549 
                   POLE 
                 
                 
                     
                   chr12 
                   133250282 
                   133250482 
                   0.517 
                   POLE 
                 
                 
                     
                   chr12 
                   133251897 
                   133252126 
                   0.600 
                   POLE 
                 
                 
                     
                   chr12 
                   133252231 
                   133252480 
                   0.512 
                   POLE 
                 
                 
                     
                   chr12 
                   133252591 
                   133252826 
                   0.470 
                   POLE 
                 
                 
                     
                   chr12 
                   133253058 
                   133253290 
                   0.502 
                   POLE 
                 
                 
                     
                   chr12 
                   133253869 
                   133254099 
                   0.429 
                   POLE 
                 
                 
                     
                   chr12 
                   133254080 
                   133254312 
                   0.502 
                   POLE 
                 
                 
                     
                   chr12 
                   133256057 
                   133256299 
                   0.494 
                   POLE 
                 
                 
                     
                   chr12 
                   133256546 
                   133256806 
                   0.441 
                   POLE 
                 
                 
                     
                   chr12 
                   133256751 
                   133257006 
                   0.469 
                   POLE 
                 
                 
                     
                   chr12 
                   133257134 
                   133257364 
                   0.429 
                   POLE 
                 
                 
                     
                   chr12 
                   133257609 
                   133257851 
                   0.523 
                   POLE 
                 
                 
                     
                   chr13 
                   28592527 
                   28592791 
                   0.434 
                   FLT3 
                 
                 
                     
                   chr13 
                   32889625 
                   32889857 
                   0.631 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32889901 
                   32890111 
                   0.583 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32890514 
                   32890741 
                   0.346 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32893139 
                   32893383 
                   0.339 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32900135 
                   32900368 
                   0.252 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32900239 
                   32900484 
                   0.305 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32900514 
                   32900762 
                   0.373 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32903445 
                   32903674 
                   0.278 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32904938 
                   32905182 
                   0.343 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32905002 
                   32905201 
                   0.315 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32905048 
                   32905165 
                   0.339 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32905048 
                   32905168 
                   0.347 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32905048 
                   32905170 
                   0.341 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32905049 
                   32905165 
                   0.342 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906224 
                   32906468 
                   0.302 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906406 
                   32906650 
                   0.310 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906408 
                   32906628 
                   0.317 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906426 
                   32906673 
                   0.306 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906464 
                   32906663 
                   0.305 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906520 
                   32906768 
                   0.317 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906575 
                   32906818 
                   0.361 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906606 
                   32906846 
                   0.378 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906668 
                   32906912 
                   0.388 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906748 
                   32906987 
                   0.388 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906815 
                   32907062 
                   0.363 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906856 
                   32907103 
                   0.367 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906893 
                   32907106 
                   0.383 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32906938 
                   32907183 
                   0.378 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32907059 
                   32907264 
                   0.374 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32907059 
                   32907307 
                   0.378 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32907288 
                   32907533 
                   0.350 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32910416 
                   32910655 
                   0.354 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32910596 
                   32910835 
                   0.388 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32910778 
                   32911027 
                   0.340 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32910967 
                   32911215 
                   0.317 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32910988 
                   32911187 
                   0.335 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32911008 
                   32911252 
                   0.331 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32911035 
                   32911252 
                   0.321 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32911045 
                   32911295 
                   0.331 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32911167 
                   32911415 
                   0.341 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32911340 
                   32911588 
                   0.333 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32911594 
                   32911838 
                   0.322 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32911841 
                   32912085 
                   0.384 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32912080 
                   32912319 
                   0.342 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32912267 
                   32912511 
                   0.265 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32912502 
                   32912746 
                   0.331 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32912749 
                   32912986 
                   0.307 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32912979 
                   32913218 
                   0.404 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32913217 
                   32913460 
                   0.336 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32913444 
                   32913691 
                   0.323 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32913682 
                   32913927 
                   0.321 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32913944 
                   32914192 
                   0.329 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32914208 
                   32914455 
                   0.347 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32914462 
                   32914709 
                   0.343 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32914691 
                   32914936 
                   0.329 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32914776 
                   32915021 
                   0.333 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32914895 
                   32915115 
                   0.326 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32914896 
                   32915115 
                   0.327 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32914906 
                   32915155 
                   0.328 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32915087 
                   32915334 
                   0.355 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32915144 
                   32915384 
                   0.357 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32918540 
                   32918787 
                   0.258 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32920834 
                   32921033 
                   0.295 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32928970 
                   32929189 
                   0.345 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32928972 
                   32929201 
                   0.357 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32928992 
                   32929236 
                   0.351 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32928996 
                   32929196 
                   0.358 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32928996 
                   32929208 
                   0.357 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32929176 
                   32929423 
                   0.339 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32929177 
                   32929426 
                   0.344 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32929220 
                   32929467 
                   0.323 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32929274 
                   32929479 
                   0.335 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32929297 
                   32929498 
                   0.322 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32930589 
                   32930789 
                   0.448 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32931650 
                   32931879 
                   0.257 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32931817 
                   32932017 
                   0.318 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32932034 
                   32932234 
                   0.313 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32936641 
                   32936885 
                   0.384 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32937319 
                   32937563 
                   0.384 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32937529 
                   32937773 
                   0.376 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32944444 
                   32944688 
                   0.359 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32945080 
                   32945249 
                   0.359 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32950820 
                   32951019 
                   0.440 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32953333 
                   32953533 
                   0.348 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32953442 
                   32953686 
                   0.363 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32953840 
                   32954084 
                   0.327 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32954054 
                   32954299 
                   0.346 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32954054 
                   32954300 
                   0.344 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32968741 
                   32968971 
                   0.359 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32968820 
                   32969069 
                   0.384 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32970989 
                   32971236 
                   0.379 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32971106 
                   32971335 
                   0.348 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32972257 
                   32972489 
                   0.373 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32972463 
                   32972703 
                   0.390 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32972600 
                   32972845 
                   0.378 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32972664 
                   32972864 
                   0.418 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32972671 
                   32972922 
                   0.397 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32972708 
                   32972954 
                   0.389 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32973392 
                   32973641 
                   0.336 
                   BRCA2 
                 
                 
                     
                   chr13 
                   32973613 
                   32973807 
                   0.267 
                   BRCA2 
                 
                 
                     
                   chr13 
                   48916668 
                   48916868 
                   0.318 
                   RB1 
                 
                 
                     
                   chr13 
                   48919151 
                   48919351 
                   0.284 
                   RB1 
                 
                 
                     
                   chr13 
                   48921945 
                   48922145 
                   0.308 
                   RB1 
                 
                 
                     
                   chr13 
                   48923001 
                   48923221 
                   0.258 
                   RB1 
                 
                 
                     
                   chr13 
                   48936897 
                   48937117 
                   0.330 
                   RB1 
                 
                 
                     
                   chr13 
                   48939068 
                   48939268 
                   0.318 
                   RB1 
                 
                 
                     
                   chr13 
                   48941560 
                   48941760 
                   0.318 
                   RB1 
                 
                 
                     
                   chr13 
                   48947429 
                   48947629 
                   0.323 
                   RB1 
                 
                 
                     
                   chr13 
                   48951017 
                   48951237 
                   0.348 
                   RB1 
                 
                 
                     
                   chr13 
                   48954364 
                   48954564 
                   0.328 
                   RB1 
                 
                 
                     
                   chr13 
                   48955326 
                   48955526 
                   0.303 
                   RB1 
                 
                 
                     
                   chr13 
                   48955536 
                   48955736 
                   0.338 
                   RB1 
                 
                 
                     
                   chr13 
                   49027033 
                   49027233 
                   0.333 
                   RB1 
                 
                 
                     
                   chr13 
                   49030212 
                   49030472 
                   0.364 
                   RB1 
                 
                 
                     
                   chr13 
                   49033792 
                   49033992 
                   0.428 
                   RB1 
                 
                 
                     
                   chr13 
                   49037854 
                   49038084 
                   0.299 
                   RB1 
                 
                 
                     
                   chr13 
                   49039190 
                   49039390 
                   0.378 
                   RB1 
                 
                 
                     
                   chr13 
                   49039267 
                   49039467 
                   0.383 
                   RB1 
                 
                 
                     
                   chr13 
                   49047356 
                   49047616 
                   0.287 
                   RB1 
                 
                 
                     
                   chr13 
                   49050783 
                   49050983 
                   0.373 
                   RB1 
                 
                 
                     
                   chr13 
                   49051484 
                   49051724 
                   0.299 
                   RB1 
                 
                 
                     
                   chr13 
                   49054133 
                   49054333 
                   0.413 
                   RB1 
                 
                 
                     
                   chr13 
                   49054700 
                   49054910 
                   0.251 
                   RB1 
                 
                 
                     
                   chr13 
                   49055078 
                   49055278 
                   0.323 
                   RB1 
                 
                 
                     
                   chr13 
                   49055456 
                   49055656 
                   0.343 
                   RB1 
                 
                 
                     
                   chr13 
                   49055834 
                   49056034 
                   0.254 
                   RB1 
                 
                 
                     
                   chr13 
                   103498123 
                   103498440 
                   0.629 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103498155 
                   103498432 
                   0.640 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103498190 
                   103498390 
                   0.642 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103498192 
                   103498440 
                   0.631 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103498192 
                   103498453 
                   0.626 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103498470 
                   103498701 
                   0.608 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103498494 
                   103498713 
                   0.618 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103498494 
                   103498717 
                   0.621 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103498574 
                   103498757 
                   0.641 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103504312 
                   103504529 
                   0.349 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103504364 
                   103504578 
                   0.372 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103506028 
                   103506230 
                   0.409 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103506526 
                   103506726 
                   0.463 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103508374 
                   103508544 
                   0.275 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103510603 
                   103510803 
                   0.393 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103513836 
                   103514056 
                   0.407 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103514321 
                   103514572 
                   0.433 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103514574 
                   103514792 
                   0.534 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103514801 
                   103515020 
                   0.482 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103515021 
                   103515221 
                   0.428 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103515235 
                   103515435 
                   0.433 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103517984 
                   103518184 
                   0.478 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103518194 
                   103518404 
                   0.412 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103518516 
                   103518726 
                   0.370 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103519057 
                   103519257 
                   0.368 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103520541 
                   103520748 
                   0.370 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103524493 
                   103524693 
                   0.413 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103524585 
                   103524802 
                   0.445 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103525496 
                   103525696 
                   0.368 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103527656 
                   103527856 
                   0.408 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103527863 
                   103528063 
                   0.408 
                   ERCC5 
                 
                 
                     
                   chr13 
                   103528070 
                   103528300 
                   0.437 
                   ERCC5 
                 
                 
                     
                   chr14 
                   38060515 
                   38060750 
                   0.589 
                   FOXA1 
                 
                 
                     
                   chr14 
                   38060564 
                   38060810 
                   0.591 
                   FOXA1 
                 
                 
                     
                   chr14 
                   38060574 
                   38060818 
                   0.592 
                   FOXA1 
                 
                 
                     
                   chr14 
                   38060586 
                   38060833 
                   0.601 
                   FOXA1 
                 
                 
                     
                   chr14 
                   45605103 
                   45605333 
                   0.558 
                   FANCM 
                 
                 
                     
                   chr14 
                   45605305 
                   45605553 
                   0.610 
                   FANCM 
                 
                 
                     
                   chr14 
                   45605573 
                   45605799 
                   0.511 
                   FANCM 
                 
                 
                     
                   chr14 
                   45606233 
                   45606433 
                   0.398 
                   FANCM 
                 
                 
                     
                   chr14 
                   45618024 
                   45618224 
                   0.363 
                   FANCM 
                 
                 
                     
                   chr14 
                   45620541 
                   45620741 
                   0.333 
                   FANCM 
                 
                 
                     
                   chr14 
                   45623034 
                   45623234 
                   0.348 
                   FANCM 
                 
                 
                     
                   chr14 
                   45628297 
                   45628497 
                   0.408 
                   FANCM 
                 
                 
                     
                   chr14 
                   45633510 
                   45633710 
                   0.373 
                   FANCM 
                 
                 
                     
                   chr14 
                   45633720 
                   45633920 
                   0.383 
                   FANCM 
                 
                 
                     
                   chr14 
                   45636166 
                   45636386 
                   0.376 
                   FANCM 
                 
                 
                     
                   chr14 
                   45639788 
                   45640013 
                   0.341 
                   FANCM 
                 
                 
                     
                   chr14 
                   45642242 
                   45642442 
                   0.403 
                   FANCM 
                 
                 
                     
                   chr14 
                   45644281 
                   45644486 
                   0.340 
                   FANCM 
                 
                 
                     
                   chr14 
                   45644653 
                   45644863 
                   0.313 
                   FANCM 
                 
                 
                     
                   chr14 
                   45644862 
                   45645099 
                   0.382 
                   FANCM 
                 
                 
                     
                   chr14 
                   45645143 
                   45645342 
                   0.350 
                   FANCM 
                 
                 
                     
                   chr14 
                   45645413 
                   45645613 
                   0.378 
                   FANCM 
                 
                 
                     
                   chr14 
                   45645666 
                   45645955 
                   0.331 
                   FANCM 
                 
                 
                     
                   chr14 
                   45645983 
                   45646183 
                   0.303 
                   FANCM 
                 
                 
                     
                   chr14 
                   45650718 
                   45650970 
                   0.332 
                   FANCM 
                 
                 
                     
                   chr14 
                   45650772 
                   45650971 
                   0.320 
                   FANCM 
                 
                 
                     
                   chr14 
                   45652886 
                   45653086 
                   0.338 
                   FANCM 
                 
                 
                     
                   chr14 
                   45654389 
                   45654589 
                   0.303 
                   FANCM 
                 
                 
                     
                   chr14 
                   45656912 
                   45657134 
                   0.269 
                   FANCM 
                 
                 
                     
                   chr14 
                   45658004 
                   45658204 
                   0.333 
                   FANCM 
                 
                 
                     
                   chr14 
                   45658183 
                   45658427 
                   0.371 
                   FANCM 
                 
                 
                     
                   chr14 
                   45658417 
                   45658644 
                   0.368 
                   FANCM 
                 
                 
                     
                   chr14 
                   45665608 
                   45665811 
                   0.348 
                   FANCM 
                 
                 
                     
                   chr14 
                   45667934 
                   45668145 
                   0.358 
                   FANCM 
                 
                 
                     
                   chr14 
                   45668983 
                   45669204 
                   0.320 
                   FANCM 
                 
                 
                     
                   chr14 
                   45669474 
                   45669678 
                   0.346 
                   FANCM 
                 
                 
                     
                   chr14 
                   95557315 
                   95557515 
                   0.313 
                   DICER1 
                 
                 
                     
                   chr14 
                   95557526 
                   95557726 
                   0.463 
                   DICER1 
                 
                 
                     
                   chr14 
                   95559982 
                   95560182 
                   0.542 
                   DICER1 
                 
                 
                     
                   chr14 
                   95560204 
                   95560434 
                   0.494 
                   DICER1 
                 
                 
                     
                   chr14 
                   95560444 
                   95560644 
                   0.398 
                   DICER1 
                 
                 
                     
                   chr14 
                   95562161 
                   95562361 
                   0.368 
                   DICER1 
                 
                 
                     
                   chr14 
                   95562361 
                   95562592 
                   0.530 
                   DICER1 
                 
                 
                     
                   chr14 
                   95562601 
                   95562801 
                   0.438 
                   DICER1 
                 
                 
                     
                   chr14 
                   95562666 
                   95562891 
                   0.398 
                   DICER1 
                 
                 
                     
                   chr14 
                   95566129 
                   95566335 
                   0.406 
                   DICER1 
                 
                 
                     
                   chr14 
                   95569682 
                   95569882 
                   0.468 
                   DICER1 
                 
                 
                     
                   chr14 
                   95569994 
                   95570194 
                   0.403 
                   DICER1 
                 
                 
                     
                   chr14 
                   95570228 
                   95570428 
                   0.418 
                   DICER1 
                 
                 
                     
                   chr14 
                   95571340 
                   95571540 
                   0.488 
                   DICER1 
                 
                 
                     
                   chr14 
                   95571974 
                   95572174 
                   0.348 
                   DICER1 
                 
                 
                     
                   chr14 
                   95572314 
                   95572514 
                   0.428 
                   DICER1 
                 
                 
                     
                   chr14 
                   95572524 
                   95572764 
                   0.249 
                   DICER1 
                 
                 
                     
                   chr14 
                   95573959 
                   95574159 
                   0.338 
                   DICER1 
                 
                 
                     
                   chr14 
                   95574168 
                   95574368 
                   0.348 
                   DICER1 
                 
                 
                     
                   chr14 
                   95574657 
                   95574857 
                   0.443 
                   DICER1 
                 
                 
                     
                   chr14 
                   95577599 
                   95577799 
                   0.433 
                   DICER1 
                 
                 
                     
                   chr14 
                   95578391 
                   95578591 
                   0.358 
                   DICER1 
                 
                 
                     
                   chr14 
                   95579340 
                   95579540 
                   0.358 
                   DICER1 
                 
                 
                     
                   chr14 
                   95581926 
                   95582126 
                   0.433 
                   DICER1 
                 
                 
                     
                   chr14 
                   95582756 
                   95582956 
                   0.358 
                   DICER1 
                 
                 
                     
                   chr14 
                   95582966 
                   95583166 
                   0.348 
                   DICER1 
                 
                 
                     
                   chr14 
                   95583900 
                   95584100 
                   0.378 
                   DICER1 
                 
                 
                     
                   chr14 
                   95590532 
                   95590732 
                   0.358 
                   DICER1 
                 
                 
                     
                   chr14 
                   95590767 
                   95590967 
                   0.393 
                   DICER1 
                 
                 
                     
                   chr14 
                   95592822 
                   95593064 
                   0.305 
                   DICER1 
                 
                 
                     
                   chr14 
                   95595734 
                   95595934 
                   0.358 
                   DICER1 
                 
                 
                     
                   chr14 
                   95596337 
                   95596537 
                   0.343 
                   DICER1 
                 
                 
                     
                   chr14 
                   95598778 
                   95598978 
                   0.383 
                   DICER1 
                 
                 
                     
                   chr14 
                   95598988 
                   95599188 
                   0.308 
                   DICER1 
                 
                 
                     
                   chr14 
                   95599591 
                   95599801 
                   0.436 
                   DICER1 
                 
                 
                     
                   chr14 
                   95623722 
                   95623973 
                   0.750 
                   DICER1 
                 
                 
                     
                   chr14 
                   105246388 
                   105246637 
                   0.596 
                   AKT1 
                 
                 
                     
                   chr14 
                   105246483 
                   105246730 
                   0.617 
                   AKT1 
                 
                 
                     
                   chr14 
                   105246501 
                   105246707 
                   0.633 
                   AKT1 
                 
                 
                     
                   chr14 
                   105246501 
                   105246745 
                   0.633 
                   AKT1 
                 
                 
                     
                   chr15 
                   32968921 
                   32969121 
                   0.303 
                   GREM1 
                 
                 
                     
                   chr15 
                   32976883 
                   32977083 
                   0.393 
                   GREM1 
                 
                 
                     
                   chr15 
                   32984845 
                   32985055 
                   0.469 
                   GREM1 
                 
                 
                     
                   chr15 
                   32988826 
                   32989036 
                   0.370 
                   SCG5 
                 
                 
                     
                   chr15 
                   33000769 
                   33000969 
                   0.512 
                   GREM1 
                 
                 
                     
                   chr15 
                   33022952 
                   33023162 
                   0.654 
                   GREM1 
                 
                 
                     
                   chr15 
                   33022952 
                   33023205 
                   0.638 
                   GREM1 
                 
                 
                     
                   chr15 
                   33023018 
                   33023279 
                   0.626 
                   GREM1 
                 
                 
                     
                   chr15 
                   33023148 
                   33023435 
                   0.521 
                   GREM1 
                 
                 
                     
                   chr15 
                   33023151 
                   33023435 
                   0.519 
                   GREM1 
                 
                 
                     
                   chr15 
                   33023205 
                   33023450 
                   0.504 
                   GREM1 
                 
                 
                     
                   chr15 
                   33023686 
                   33023886 
                   0.517 
                   GREM1 
                 
                 
                     
                   chr15 
                   33024084 
                   33024294 
                   0.464 
                   GREM1 
                 
                 
                     
                   chr15 
                   33024482 
                   33024682 
                   0.398 
                   GREM1 
                 
                 
                     
                   chr15 
                   33026472 
                   33026672 
                   0.299 
                   GREM1 
                 
                 
                     
                   chr15 
                   66727327 
                   66727566 
                   0.546 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66727339 
                   66727587 
                   0.550 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66727339 
                   66727588 
                   0.548 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66727359 
                   66727598 
                   0.542 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66729024 
                   66729277 
                   0.496 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66729065 
                   66729264 
                   0.515 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66774016 
                   66774220 
                   0.527 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66774016 
                   66774260 
                   0.510 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66774048 
                   66774260 
                   0.516 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66774052 
                   66774260 
                   0.517 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66777305 
                   66777541 
                   0.591 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66777336 
                   66777568 
                   0.597 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66777336 
                   66777570 
                   0.600 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   66777338 
                   66777568 
                   0.597 
                   MAP2K1 
                 
                 
                     
                   chr15 
                   89787224 
                   89787484 
                   0.651 
                   FANCI 
                 
                 
                     
                   chr15 
                   89790756 
                   89790956 
                   0.368 
                   FANCI 
                 
                 
                     
                   chr15 
                   89801818 
                   89802048 
                   0.403 
                   FANCI 
                 
                 
                     
                   chr15 
                   89803854 
                   89804054 
                   0.403 
                   FANCI 
                 
                 
                     
                   chr15 
                   89804662 
                   89804884 
                   0.372 
                   FANCI 
                 
                 
                     
                   chr15 
                   89804949 
                   89805159 
                   0.365 
                   FANCI 
                 
                 
                     
                   chr15 
                   89806635 
                   89806874 
                   0.371 
                   FANCI 
                 
                 
                     
                   chr15 
                   89807040 
                   89807240 
                   0.403 
                   FANCI 
                 
                 
                     
                   chr15 
                   89807671 
                   89807891 
                   0.344 
                   FANCI 
                 
                 
                     
                   chr15 
                   89811673 
                   89811922 
                   0.364 
                   FANCI 
                 
                 
                     
                   chr15 
                   89817473 
                   89817702 
                   0.370 
                   FANCI 
                 
                 
                     
                   chr15 
                   89819937 
                   89820137 
                   0.418 
                   FANCI 
                 
                 
                     
                   chr15 
                   89821824 
                   89822080 
                   0.358 
                   FANCI 
                 
                 
                     
                   chr15 
                   89824311 
                   89824511 
                   0.333 
                   FANCI 
                 
                 
                     
                   chr15 
                   89824830 
                   89825066 
                   0.359 
                   FANCI 
                 
                 
                     
                   chr15 
                   89828191 
                   89828429 
                   0.439 
                   FANCI 
                 
                 
                     
                   chr15 
                   89833373 
                   89833592 
                   0.368 
                   FANCI 
                 
                 
                     
                   chr15 
                   89834739 
                   89834949 
                   0.365 
                   FANCI 
                 
                 
                     
                   chr15 
                   89835684 
                   89835936 
                   0.336 
                   FANCI 
                 
                 
                     
                   chr15 
                   89836099 
                   89836321 
                   0.327 
                   FANCI 
                 
                 
                     
                   chr15 
                   89837021 
                   89837221 
                   0.358 
                   FANCI 
                 
                 
                     
                   chr15 
                   89838207 
                   89838356 
                   0.480 
                   FANCI 
                 
                 
                     
                   chr15 
                   89843116 
                   89843345 
                   0.417 
                   FANCI 
                 
                 
                     
                   chr15 
                   89843449 
                   89843649 
                   0.403 
                   FANCI 
                 
                 
                     
                   chr15 
                   89844490 
                   89844700 
                   0.455 
                   FANCI 
                 
                 
                     
                   chr15 
                   89846965 
                   89847165 
                   0.388 
                   FANCI 
                 
                 
                     
                   chr15 
                   89848390 
                   89848629 
                   0.479 
                   FANCI 
                 
                 
                     
                   chr15 
                   89848727 
                   89848927 
                   0.478 
                   FANCI 
                 
                 
                     
                   chr15 
                   89849176 
                   89849396 
                   0.439 
                   FANCI 
                 
                 
                     
                   chr15 
                   89850578 
                   89850778 
                   0.403 
                   FANCI 
                 
                 
                     
                   chr15 
                   89850795 
                   89850995 
                   0.438 
                   FANCI 
                 
                 
                     
                   chr15 
                   89857735 
                   89857935 
                   0.398 
                   FANCI 
                 
                 
                     
                   chr15 
                   89858460 
                   89858694 
                   0.498 
                   FANCI 
                 
                 
                     
                   chr15 
                   89859420 
                   89859663 
                   0.430 
                   FANCI 
                 
                 
                     
                   chr15 
                   89859773 
                   89859973 
                   0.517 
                   FANCI 
                 
                 
                     
                   chr15 
                   89859992 
                   89860192 
                   0.443 
                   FANCI 
                 
                 
                     
                   chr15 
                   89860258 
                   89860477 
                   0.359 
                   FANCI 
                 
                 
                     
                   chr15 
                   90631785 
                   90632007 
                   0.570 
                   IDH2 
                 
                 
                     
                   chr15 
                   90631814 
                   90632043 
                   0.548 
                   IDH2 
                 
                 
                     
                   chr15 
                   90631843 
                   90632054 
                   0.519 
                   IDH2 
                 
                 
                     
                   chr16 
                   3631168 
                   3631388 
                   0.443 
                   SLX4 
                 
                 
                     
                   chr16 
                   3632424 
                   3632665 
                   0.645 
                   SLX4 
                 
                 
                     
                   chr16 
                   3632693 
                   3632893 
                   0.597 
                   SLX4 
                 
                 
                     
                   chr16 
                   3633083 
                   3633283 
                   0.582 
                   SLX4 
                 
                 
                     
                   chr16 
                   3633339 
                   3633565 
                   0.590 
                   SLX4 
                 
                 
                     
                   chr16 
                   3634696 
                   3634896 
                   0.502 
                   SLX4 
                 
                 
                     
                   chr16 
                   3639002 
                   3639202 
                   0.617 
                   SLX4 
                 
                 
                     
                   chr16 
                   3639197 
                   3639423 
                   0.652 
                   SLX4 
                 
                 
                     
                   chr16 
                   3639505 
                   3639754 
                   0.632 
                   SLX4 
                 
                 
                     
                   chr16 
                   3639692 
                   3639932 
                   0.639 
                   SLX4 
                 
                 
                     
                   chr16 
                   3639911 
                   3640159 
                   0.530 
                   SLX4 
                 
                 
                     
                   chr16 
                   3640185 
                   3640409 
                   0.498 
                   SLX4 
                 
                 
                     
                   chr16 
                   3640478 
                   3640721 
                   0.607 
                   SLX4 
                 
                 
                     
                   chr16 
                   3640760 
                   3641047 
                   0.660 
                   SLX4 
                 
                 
                     
                   chr16 
                   3641072 
                   3641272 
                   0.468 
                   SLX4 
                 
                 
                     
                   chr16 
                   3642628 
                   3642858 
                   0.597 
                   SLX4 
                 
                 
                     
                   chr16 
                   3644537 
                   3644773 
                   0.608 
                   SLX4 
                 
                 
                     
                   chr16 
                   3645495 
                   3645705 
                   0.673 
                   SLX4 
                 
                 
                     
                   chr16 
                   3646003 
                   3646244 
                   0.698 
                   SLX4 
                 
                 
                     
                   chr16 
                   3646031 
                   3646244 
                   0.720 
                   SLX4 
                 
                 
                     
                   chr16 
                   3646124 
                   3646405 
                   0.699 
                   SLX4 
                 
                 
                     
                   chr16 
                   3646149 
                   3646391 
                   0.712 
                   SLX4 
                 
                 
                     
                   chr16 
                   3646157 
                   3646403 
                   0.704 
                   SLX4 
                 
                 
                     
                   chr16 
                   3647312 
                   3647583 
                   0.610 
                   SLX4 
                 
                 
                     
                   chr16 
                   3647601 
                   3647800 
                   0.540 
                   SLX4 
                 
                 
                     
                   chr16 
                   3647864 
                   3648074 
                   0.578 
                   SLX4 
                 
                 
                     
                   chr16 
                   3650971 
                   3651251 
                   0.530 
                   SLX4 
                 
                 
                     
                   chr16 
                   3652058 
                   3652258 
                   0.557 
                   SLX4 
                 
                 
                     
                   chr16 
                   3656390 
                   3656622 
                   0.506 
                   SLX4 
                 
                 
                     
                   chr16 
                   3656642 
                   3656842 
                   0.443 
                   SLX4 
                 
                 
                     
                   chr16 
                   3658480 
                   3658725 
                   0.528 
                   SLX4 
                 
                 
                     
                   chr16 
                   3658510 
                   3658671 
                   0.562 
                   SLX4 
                 
                 
                     
                   chr16 
                   3658784 
                   3659014 
                   0.455 
                   SLX4 
                 
                 
                     
                   chr16 
                   3659560 
                   3659760 
                   0.438 
                   SLX4 
                 
                 
                     
                   chr16 
                   14013935 
                   14014175 
                   0.651 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14013966 
                   14014166 
                   0.662 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14013970 
                   14014170 
                   0.662 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14013971 
                   14014170 
                   0.665 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14015823 
                   14016023 
                   0.373 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14016033 
                   14016243 
                   0.355 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14020466 
                   14020710 
                   0.351 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14021912 
                   14022151 
                   0.338 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14024532 
                   14024732 
                   0.373 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14025949 
                   14026157 
                   0.344 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14027949 
                   14028149 
                   0.348 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14028984 
                   14029224 
                   0.415 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14029445 
                   14029685 
                   0.452 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14031514 
                   14031714 
                   0.373 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14038575 
                   14038734 
                   0.494 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14041470 
                   14041670 
                   0.468 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14041655 
                   14041919 
                   0.509 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14041900 
                   14042126 
                   0.498 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14042120 
                   14042369 
                   0.404 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14042584 
                   14042854 
                   0.424 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14042844 
                   14043078 
                   0.336 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14042902 
                   14043146 
                   0.347 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14043430 
                   14043679 
                   0.284 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14044214 
                   14044436 
                   0.332 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14045149 
                   14045380 
                   0.276 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14045389 
                   14045634 
                   0.427 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14045727 
                   14045927 
                   0.328 
                   ERCC4 
                 
                 
                     
                   chr16 
                   14046154 
                   14046384 
                   0.303 
                   ERCC4 
                 
                 
                     
                   chr16 
                   23614570 
                   23614827 
                   0.310 
                   PALB2 
                 
                 
                     
                   chr16 
                   23614836 
                   23615076 
                   0.407 
                   PALB2 
                 
                 
                     
                   chr16 
                   23619110 
                   23619349 
                   0.479 
                   PALB2 
                 
                 
                     
                   chr16 
                   23625213 
                   23625413 
                   0.398 
                   PALB2 
                 
                 
                     
                   chr16 
                   23632741 
                   23632891 
                   0.391 
                   PALB2 
                 
                 
                     
                   chr16 
                   23634215 
                   23634415 
                   0.393 
                   PALB2 
                 
                 
                     
                   chr16 
                   23635260 
                   23635465 
                   0.374 
                   PALB2 
                 
                 
                     
                   chr16 
                   23637513 
                   23637713 
                   0.458 
                   PALB2 
                 
                 
                     
                   chr16 
                   23640440 
                   23640682 
                   0.370 
                   PALB2 
                 
                 
                     
                   chr16 
                   23640927 
                   23641175 
                   0.470 
                   PALB2 
                 
                 
                     
                   chr16 
                   23641292 
                   23641502 
                   0.431 
                   PALB2 
                 
                 
                     
                   chr16 
                   23641570 
                   23641813 
                   0.385 
                   PALB2 
                 
                 
                     
                   chr16 
                   23646217 
                   23646416 
                   0.470 
                   PALB2 
                 
                 
                     
                   chr16 
                   23646250 
                   23646449 
                   0.460 
                   PALB2 
                 
                 
                     
                   chr16 
                   23646427 
                   23646636 
                   0.390 
                   PALB2 
                 
                 
                     
                   chr16 
                   23646623 
                   23646823 
                   0.403 
                   PALB2 
                 
                 
                     
                   chr16 
                   23646780 
                   23647008 
                   0.345 
                   PALB2 
                 
                 
                     
                   chr16 
                   23646984 
                   23647228 
                   0.400 
                   PALB2 
                 
                 
                     
                   chr16 
                   23647144 
                   23647434 
                   0.385 
                   PALB2 
                 
                 
                     
                   chr16 
                   23647358 
                   23647558 
                   0.483 
                   PALB2 
                 
                 
                     
                   chr16 
                   23647369 
                   23647610 
                   0.467 
                   PALB2 
                 
                 
                     
                   chr16 
                   23649127 
                   23649357 
                   0.355 
                   PALB2 
                 
                 
                     
                   chr16 
                   23649265 
                   23649465 
                   0.358 
                   PALB2 
                 
                 
                     
                   chr16 
                   23652430 
                   23652650 
                   0.692 
                   PALB2 
                 
                 
                     
                   chr16 
                   23652647 
                   23652887 
                   0.647 
                   PALB2 
                 
                 
                     
                   chr16 
                   68772169 
                   68772389 
                   0.679 
                   CDH1 
                 
                 
                     
                   chr16 
                   68835529 
                   68835729 
                   0.463 
                   CDH1 
                 
                 
                     
                   chr16 
                   68835564 
                   68835767 
                   0.485 
                   CDH1 
                 
                 
                     
                   chr16 
                   68842243 
                   68842453 
                   0.469 
                   CDH1 
                 
                 
                     
                   chr16 
                   68842518 
                   68842718 
                   0.423 
                   CDH1 
                 
                 
                     
                   chr16 
                   68844017 
                   68844227 
                   0.512 
                   CDH1 
                 
                 
                     
                   chr16 
                   68845519 
                   68845719 
                   0.483 
                   CDH1 
                 
                 
                     
                   chr16 
                   68845706 
                   68845945 
                   0.517 
                   CDH1 
                 
                 
                     
                   chr16 
                   68845947 
                   68846147 
                   0.502 
                   CDH1 
                 
                 
                     
                   chr16 
                   68846157 
                   68846377 
                   0.416 
                   CDH1 
                 
                 
                     
                   chr16 
                   68847216 
                   68847450 
                   0.477 
                   CDH1 
                 
                 
                     
                   chr16 
                   68849385 
                   68849585 
                   0.488 
                   CDH1 
                 
                 
                     
                   chr16 
                   68849423 
                   68849649 
                   0.529 
                   CDH1 
                 
                 
                     
                   chr16 
                   68853169 
                   68853348 
                   0.522 
                   CDH1 
                 
                 
                     
                   chr16 
                   68855861 
                   68856061 
                   0.453 
                   CDH1 
                 
                 
                     
                   chr16 
                   68856071 
                   68856271 
                   0.488 
                   CDH1 
                 
                 
                     
                   chr16 
                   68856802 
                   68857067 
                   0.560 
                   CDH1 
                 
                 
                     
                   chr16 
                   68857287 
                   68857494 
                   0.481 
                   CDH1 
                 
                 
                     
                   chr16 
                   68862023 
                   68862255 
                   0.511 
                   CDH1 
                 
                 
                     
                   chr16 
                   68863473 
                   68863683 
                   0.488 
                   CDH1 
                 
                 
                     
                   chr16 
                   68867121 
                   68867366 
                   0.488 
                   CDH1 
                 
                 
                     
                   chr16 
                   68867369 
                   68867599 
                   0.476 
                   CDH1 
                 
                 
                     
                   chr16 
                   89804046 
                   89804215 
                   0.553 
                   FANCA 
                 
                 
                     
                   chr16 
                   89804303 
                   89804513 
                   0.592 
                   FANCA 
                 
                 
                     
                   chr16 
                   89804648 
                   89804858 
                   0.635 
                   FANCA 
                 
                 
                     
                   chr16 
                   89804928 
                   89805172 
                   0.596 
                   FANCA 
                 
                 
                     
                   chr16 
                   89805241 
                   89805441 
                   0.498 
                   FANCA 
                 
                 
                     
                   chr16 
                   89805462 
                   89805662 
                   0.612 
                   FANCA 
                 
                 
                     
                   chr16 
                   89805672 
                   89805892 
                   0.548 
                   FANCA 
                 
                 
                     
                   chr16 
                   89806299 
                   89806509 
                   0.502 
                   FANCA 
                 
                 
                     
                   chr16 
                   89807188 
                   89807437 
                   0.364 
                   FANCA 
                 
                 
                     
                   chr16 
                   89809197 
                   89809432 
                   0.542 
                   FANCA 
                 
                 
                     
                   chr16 
                   89811314 
                   89811494 
                   0.646 
                   FANCA 
                 
                 
                     
                   chr16 
                   89812889 
                   89813109 
                   0.557 
                   FANCA 
                 
                 
                     
                   chr16 
                   89813161 
                   89813385 
                   0.551 
                   FANCA 
                 
                 
                     
                   chr16 
                   89814966 
                   89815166 
                   0.587 
                   FANCA 
                 
                 
                     
                   chr16 
                   89816227 
                   89816392 
                   0.608 
                   FANCA 
                 
                 
                     
                   chr16 
                   89818546 
                   89818699 
                   0.416 
                   FANCA 
                 
                 
                     
                   chr16 
                   89825033 
                   89825256 
                   0.563 
                   FANCA 
                 
                 
                     
                   chr16 
                   89825068 
                   89825276 
                   0.545 
                   FANCA 
                 
                 
                     
                   chr16 
                   89828413 
                   89828604 
                   0.396 
                   FANCA 
                 
                 
                     
                   chr16 
                   89831297 
                   89831493 
                   0.533 
                   FANCA 
                 
                 
                     
                   chr16 
                   89833531 
                   89833695 
                   0.358 
                   FANCA 
                 
                 
                     
                   chr16 
                   89836321 
                   89836521 
                   0.617 
                   FANCA 
                 
                 
                     
                   chr16 
                   89836550 
                   89836790 
                   0.598 
                   FANCA 
                 
                 
                     
                   chr16 
                   89836823 
                   89837062 
                   0.604 
                   FANCA 
                 
                 
                     
                   chr16 
                   89836842 
                   89837075 
                   0.615 
                   FANCA 
                 
                 
                     
                   chr16 
                   89836876 
                   89837138 
                   0.635 
                   FANCA 
                 
                 
                     
                   chr16 
                   89836882 
                   89837082 
                   0.627 
                   FANCA 
                 
                 
                     
                   chr16 
                   89836894 
                   89837156 
                   0.627 
                   FANCA 
                 
                 
                     
                   chr16 
                   89838040 
                   89838261 
                   0.514 
                   FANCA 
                 
                 
                     
                   chr16 
                   89839593 
                   89839838 
                   0.573 
                   FANCA 
                 
                 
                     
                   chr16 
                   89842062 
                   89842262 
                   0.498 
                   FANCA 
                 
                 
                     
                   chr16 
                   89845140 
                   89845350 
                   0.483 
                   FANCA 
                 
                 
                     
                   chr16 
                   89845256 
                   89845456 
                   0.527 
                   FANCA 
                 
                 
                     
                   chr16 
                   89846317 
                   89846557 
                   0.498 
                   FANCA 
                 
                 
                     
                   chr16 
                   89849141 
                   89849341 
                   0.502 
                   FANCA 
                 
                 
                     
                   chr16 
                   89849323 
                   89849591 
                   0.554 
                   FANCA 
                 
                 
                     
                   chr16 
                   89857774 
                   89858016 
                   0.560 
                   FANCA 
                 
                 
                     
                   chr16 
                   89858250 
                   89858450 
                   0.567 
                   FANCA 
                 
                 
                     
                   chr16 
                   89858752 
                   89858951 
                   0.555 
                   FANCA 
                 
                 
                     
                   chr16 
                   89862215 
                   89862425 
                   0.512 
                   FANCA 
                 
                 
                     
                   chr16 
                   89865452 
                   89865652 
                   0.532 
                   FANCA 
                 
                 
                     
                   chr16 
                   89865648 
                   89865886 
                   0.498 
                   FANCA 
                 
                 
                     
                   chr16 
                   89865874 
                   89866074 
                   0.408 
                   FANCA 
                 
                 
                     
                   chr16 
                   89869678 
                   89869909 
                   0.461 
                   FANCA 
                 
                 
                     
                   chr16 
                   89871619 
                   89871819 
                   0.522 
                   FANCA 
                 
                 
                     
                   chr16 
                   89874567 
                   89874718 
                   0.375 
                   FANCA 
                 
                 
                     
                   chr16 
                   89877021 
                   89877274 
                   0.382 
                   FANCA 
                 
                 
                     
                   chr16 
                   89877278 
                   89877525 
                   0.520 
                   FANCA 
                 
                 
                     
                   chr16 
                   89880876 
                   89881036 
                   0.342 
                   FANCA 
                 
                 
                     
                   chr16 
                   89882268 
                   89882508 
                   0.564 
                   FANCA 
                 
                 
                     
                   chr17 
                   7572710 
                   7572941 
                   0.547 
                   TP53 
                 
                 
                     
                   chr17 
                   7572841 
                   7573094 
                   0.524 
                   TP53 
                 
                 
                     
                   chr17 
                   7573785 
                   7574015 
                   0.571 
                   TP53 
                 
                 
                     
                   chr17 
                   7573785 
                   7574050 
                   0.583 
                   TP53 
                 
                 
                     
                   chr17 
                   7573803 
                   7574050 
                   0.593 
                   TP53 
                 
                 
                     
                   chr17 
                   7573811 
                   7574017 
                   0.580 
                   TP53 
                 
                 
                     
                   chr17 
                   7576734 
                   7576934 
                   0.468 
                   TP53 
                 
                 
                     
                   chr17 
                   7576933 
                   7577155 
                   0.552 
                   TP53 
                 
                 
                     
                   chr17 
                   7576951 
                   7577151 
                   0.557 
                   TP53 
                 
                 
                     
                   chr17 
                   7576970 
                   7577197 
                   0.548 
                   TP53 
                 
                 
                     
                   chr17 
                   7576998 
                   7577191 
                   0.552 
                   TP53 
                 
                 
                     
                   chr17 
                   7576998 
                   7577241 
                   0.529 
                   TP53 
                 
                 
                     
                   chr17 
                   7576998 
                   7577242 
                   0.531 
                   TP53 
                 
                 
                     
                   chr17 
                   7577014 
                   7577263 
                   0.532 
                   TP53 
                 
                 
                     
                   chr17 
                   7577304 
                   7577572 
                   0.565 
                   TP53 
                 
                 
                     
                   chr17 
                   7577329 
                   7577570 
                   0.574 
                   TP53 
                 
                 
                     
                   chr17 
                   7577329 
                   7577576 
                   0.569 
                   TP53 
                 
                 
                     
                   chr17 
                   7577346 
                   7577570 
                   0.596 
                   TP53 
                 
                 
                     
                   chr17 
                   7577346 
                   7577576 
                   0.589 
                   TP53 
                 
                 
                     
                   chr17 
                   7577371 
                   7577620 
                   0.564 
                   TP53 
                 
                 
                     
                   chr17 
                   7577398 
                   7577598 
                   0.572 
                   TP53 
                 
                 
                     
                   chr17 
                   7578196 
                   7578426 
                   0.563 
                   TP53 
                 
                 
                     
                   chr17 
                   7578263 
                   7578502 
                   0.629 
                   TP53 
                 
                 
                     
                   chr17 
                   7578283 
                   7578494 
                   0.637 
                   TP53 
                 
                 
                     
                   chr17 
                   7578298 
                   7578566 
                   0.617 
                   TP53 
                 
                 
                     
                   chr17 
                   7578299 
                   7578502 
                   0.642 
                   TP53 
                 
                 
                     
                   chr17 
                   7578363 
                   7578562 
                   0.615 
                   TP53 
                 
                 
                     
                   chr17 
                   7578363 
                   7578598 
                   0.597 
                   TP53 
                 
                 
                     
                   chr17 
                   7579266 
                   7579515 
                   0.624 
                   TP53 
                 
                 
                     
                   chr17 
                   7579311 
                   7579460 
                   0.620 
                   TP53 
                 
                 
                     
                   chr17 
                   7579326 
                   7579526 
                   0.627 
                   TP53 
                 
                 
                     
                   chr17 
                   7579332 
                   7579550 
                   0.616 
                   TP53 
                 
                 
                     
                   chr17 
                   7579817 
                   7579987 
                   0.556 
                   TP53 
                 
                 
                     
                   chr17 
                   7590681 
                   7590919 
                   0.573 
                   TP53 
                 
                 
                     
                   chr17 
                   33426833 
                   33427064 
                   0.474 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33427044 
                   33427283 
                   0.500 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33427269 
                   33427513 
                   0.437 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33427477 
                   33427725 
                   0.518 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33427706 
                   33427935 
                   0.504 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33427916 
                   33428162 
                   0.498 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33428100 
                   33428345 
                   0.577 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33430196 
                   33430419 
                   0.567 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33430401 
                   33430620 
                   0.573 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33433344 
                   33433506 
                   0.564 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33433897 
                   33434133 
                   0.489 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33434295 
                   33434532 
                   0.500 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33445499 
                   33445672 
                   0.586 
                   RAD51D 
                 
                 
                     
                   chr17 
                   33446550 
                   33446780 
                   0.662 
                   RAD51D 
                 
                 
                     
                   chr17 
                   37868175 
                   37868423 
                   0.606 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37868177 
                   37868424 
                   0.605 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37868184 
                   37868432 
                   0.614 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37868192 
                   37868432 
                   0.622 
                   ERBB2 
                 
                 
                     
                   chr17 
                   41226314 
                   41226567 
                   0.433 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41228463 
                   41228682 
                   0.368 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41231290 
                   41231560 
                   0.432 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41234185 
                   41234455 
                   0.435 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41234392 
                   41234631 
                   0.438 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41242906 
                   41243146 
                   0.444 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41243450 
                   41243690 
                   0.411 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41243675 
                   41243921 
                   0.397 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41243914 
                   41244153 
                   0.433 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41244048 
                   41244300 
                   0.368 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41244075 
                   41244265 
                   0.366 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41244473 
                   41244712 
                   0.371 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41244534 
                   41244778 
                   0.376 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41244766 
                   41245013 
                   0.387 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41245011 
                   41245240 
                   0.409 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41245209 
                   41245462 
                   0.374 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41245347 
                   41245586 
                   0.404 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41245598 
                   41245827 
                   0.370 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41245825 
                   41246064 
                   0.375 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41246061 
                   41246310 
                   0.376 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41246304 
                   41246553 
                   0.416 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41246534 
                   41246786 
                   0.423 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41246546 
                   41246786 
                   0.427 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41246595 
                   41246842 
                   0.419 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41246643 
                   41246890 
                   0.403 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41246709 
                   41246956 
                   0.379 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41246794 
                   41247027 
                   0.338 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41247801 
                   41248006 
                   0.403 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41249211 
                   41249311 
                   0.356 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41251673 
                   41251893 
                   0.380 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41251732 
                   41251945 
                   0.397 
                   BRCA1 
                 
                 
                     
                   chr17 
                   37880017 
                   37880264 
                   0.528 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37880031 
                   37880255 
                   0.524 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37880061 
                   37880274 
                   0.505 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37880069 
                   37880274 
                   0.500 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37880955 
                   37881196 
                   0.595 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37880969 
                   37881216 
                   0.589 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37880974 
                   37881216 
                   0.593 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37880983 
                   37881227 
                   0.592 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37881166 
                   37881380 
                   0.609 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37881201 
                   37881450 
                   0.584 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37881273 
                   37881520 
                   0.573 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37881304 
                   37881521 
                   0.573 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37881453 
                   37881652 
                   0.595 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37881465 
                   37881668 
                   0.598 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37881510 
                   37881737 
                   0.601 
                   ERBB2 
                 
                 
                     
                   chr17 
                   37881598 
                   37881798 
                   0.632 
                   ERBB2 
                 
                 
                     
                   chr17 
                   41196311 
                   41196511 
                   0.393 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41197220 
                   41197464 
                   0.429 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41197314 
                   41197566 
                   0.419 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41197571 
                   41197819 
                   0.550 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41199637 
                   41199729 
                   0.559 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41201055 
                   41201304 
                   0.476 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41202997 
                   41203243 
                   0.449 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41209041 
                   41209195 
                   0.445 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41215338 
                   41215577 
                   0.433 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41215806 
                   41216045 
                   0.375 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41219623 
                   41219726 
                   0.337 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41222828 
                   41223088 
                   0.402 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41222835 
                   41223088 
                   0.406 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41222885 
                   41223141 
                   0.444 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41223090 
                   41223269 
                   0.494 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41256181 
                   41256358 
                   0.315 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41256830 
                   41257034 
                   0.376 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41256884 
                   41257140 
                   0.339 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41258410 
                   41258681 
                   0.324 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41267598 
                   41267807 
                   0.371 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41267602 
                   41267807 
                   0.369 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41267603 
                   41267794 
                   0.354 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41267603 
                   41267834 
                   0.371 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41267630 
                   41267779 
                   0.353 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41267645 
                   41267836 
                   0.391 
                   BRCA1 
                 
                 
                     
                   chr17 
                   41275961 
                   41276197 
                   0.312 
                   BRCA1 
                 
                 
                     
                   chr17 
                   46805588 
                   46805837 
                   0.672 
                   HOXB13 
                 
                 
                     
                   chr17 
                   47696239 
                   47696485 
                   0.453 
                   SPOP 
                 
                 
                     
                   chr17 
                   47696300 
                   47696545 
                   0.455 
                   SPOP 
                 
                 
                     
                   chr17 
                   47696324 
                   47696565 
                   0.442 
                   SPOP 
                 
                 
                     
                   chr17 
                   47696359 
                   47696607 
                   0.422 
                   SPOP 
                 
                 
                     
                   chr17 
                   47696424 
                   47696669 
                   0.415 
                   SPOP 
                 
                 
                     
                   chr17 
                   47696450 
                   47696669 
                   0.405 
                   SPOP 
                 
                 
                     
                   chr17 
                   47696450 
                   47696689 
                   0.413 
                   SPOP 
                 
                 
                     
                   chr17 
                   47696486 
                   47696715 
                   0.387 
                   SPOP 
                 
                 
                     
                   chr17 
                   56769976 
                   56770175 
                   0.590 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56772289 
                   56772542 
                   0.421 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56773994 
                   56774243 
                   0.404 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56780486 
                   56780723 
                   0.345 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56787247 
                   56787446 
                   0.365 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56787285 
                   56787460 
                   0.341 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56798102 
                   56798172 
                   0.352 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56801331 
                   56801553 
                   0.390 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56809830 
                   56810049 
                   0.382 
                   RAD51C 
                 
                 
                     
                   chr17 
                   56811478 
                   56811716 
                   0.385 
                   RAD51C 
                 
                 
                     
                   chr17 
                   59756779 
                   59756979 
                   0.313 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59759726 
                   59759955 
                   0.252 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59760615 
                   59760854 
                   0.308 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59760809 
                   59761044 
                   0.335 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59761001 
                   59761201 
                   0.353 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59761265 
                   59761494 
                   0.413 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59761395 
                   59761636 
                   0.343 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59763229 
                   59763449 
                   0.357 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59763460 
                   59763660 
                   0.338 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59770816 
                   59771046 
                   0.307 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59793106 
                   59793349 
                   0.316 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59793137 
                   59793367 
                   0.338 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59820379 
                   59820551 
                   0.393 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59821796 
                   59821945 
                   0.373 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59853687 
                   59853887 
                   0.353 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59857537 
                   59857737 
                   0.333 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59858201 
                   59858428 
                   0.355 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59861553 
                   59861773 
                   0.326 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59870956 
                   59871190 
                   0.345 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59876405 
                   59876605 
                   0.388 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59876622 
                   59876822 
                   0.284 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59878569 
                   59878769 
                   0.413 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59878611 
                   59878844 
                   0.397 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59885818 
                   59886038 
                   0.439 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59886058 
                   59886268 
                   0.346 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59924485 
                   59924714 
                   0.348 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59926478 
                   59926707 
                   0.348 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59934381 
                   59934581 
                   0.383 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59937155 
                   59937392 
                   0.374 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59938714 
                   59938914 
                   0.333 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59940627 
                   59940827 
                   0.577 
                   BRIP1 
                 
                 
                     
                   chr17 
                   59940844 
                   59941054 
                   0.592 
                   BRIP1 
                 
                 
                     
                   chr18 
                   48556368 
                   48556604 
                   0.692 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48556368 
                   48556608 
                   0.689 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48556413 
                   48556612 
                   0.680 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48556414 
                   48556616 
                   0.675 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48573249 
                   48573492 
                   0.328 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48573500 
                   48573738 
                   0.364 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48575147 
                   48575346 
                   0.340 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48575524 
                   48575724 
                   0.294 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48581203 
                   48581433 
                   0.455 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48581249 
                   48581498 
                   0.428 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48584399 
                   48584599 
                   0.443 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48584673 
                   48584893 
                   0.439 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48586106 
                   48586306 
                   0.308 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48591791 
                   48592035 
                   0.408 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48593378 
                   48593608 
                   0.407 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48602902 
                   48603166 
                   0.430 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48602922 
                   48603132 
                   0.445 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48603000 
                   48603249 
                   0.424 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48603132 
                   48603332 
                   0.289 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48604566 
                   48604815 
                   0.488 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48604617 
                   48604861 
                   0.490 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48604640 
                   48604881 
                   0.492 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48604711 
                   48604957 
                   0.421 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48605303 
                   48605503 
                   0.294 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48605551 
                   48605798 
                   0.351 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48605981 
                   48606181 
                   0.318 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48606203 
                   48606477 
                   0.349 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48606469 
                   48606712 
                   0.357 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48607311 
                   48607586 
                   0.326 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48607638 
                   48607926 
                   0.412 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48608009 
                   48608208 
                   0.375 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48608225 
                   48608485 
                   0.368 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48608754 
                   48608904 
                   0.450 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48609535 
                   48609685 
                   0.470 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48609670 
                   48609869 
                   0.355 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48610653 
                   48610803 
                   0.358 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48610833 
                   48611078 
                   0.488 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48611097 
                   48611339 
                   0.490 
                   SMAD4 
                 
                 
                     
                   chr18 
                   48611405 
                   48611605 
                   0.353 
                   SMAD4 
                 
                 
                     
                   chr19 
                   1206543 
                   1206797 
                   0.643 
                   STK11 
                 
                 
                     
                   chr19 
                   1206613 
                   1206843 
                   0.558 
                   STK11 
                 
                 
                     
                   chr19 
                   1206770 
                   1207017 
                   0.560 
                   STK11 
                 
                 
                     
                   chr19 
                   1206962 
                   1207206 
                   0.596 
                   STK11 
                 
                 
                     
                   chr19 
                   1218302 
                   1218502 
                   0.532 
                   STK11 
                 
                 
                     
                   chr19 
                   1219161 
                   1219399 
                   0.653 
                   STK11 
                 
                 
                     
                   chr19 
                   1220251 
                   1220492 
                   0.632 
                   STK11 
                 
                 
                     
                   chr19 
                   1220276 
                   1220492 
                   0.636 
                   STK11 
                 
                 
                     
                   chr19 
                   1220475 
                   1220701 
                   0.705 
                   STK11 
                 
                 
                     
                   chr19 
                   1220502 
                   1220701 
                   0.715 
                   STK11 
                 
                 
                     
                   chr19 
                   1220681 
                   1220938 
                   0.647 
                   STK11 
                 
                 
                     
                   chr19 
                   1220681 
                   1220941 
                   0.648 
                   STK11 
                 
                 
                     
                   chr19 
                   1221151 
                   1221351 
                   0.582 
                   STK11 
                 
                 
                     
                   chr19 
                   1221821 
                   1222071 
                   0.685 
                   STK11 
                 
                 
                     
                   chr19 
                   1222984 
                   1223224 
                   0.643 
                   STK11 
                 
                 
                     
                   chr19 
                   1226453 
                   1226708 
                   0.715 
                   STK11 
                 
                 
                     
                   chr19 
                   1226464 
                   1226754 
                   0.704 
                   STK11 
                 
                 
                     
                   chr19 
                   1226465 
                   1226707 
                   0.716 
                   STK11 
                 
                 
                     
                   chr19 
                   1228261 
                   1228461 
                   0.547 
                   STK11 
                 
                 
                     
                   chr19 
                   3114798 
                   3115046 
                   0.683 
                   GNA11 
                 
                 
                     
                   chr19 
                   3114798 
                   3115049 
                   0.683 
                   GNA11 
                 
                 
                     
                   chr19 
                   3114839 
                   3115040 
                   0.688 
                   GNA11 
                 
                 
                     
                   chr19 
                   3114841 
                   3115040 
                   0.685 
                   GNA11 
                 
                 
                     
                   chr19 
                   3118772 
                   3118996 
                   0.622 
                   GNA11 
                 
                 
                     
                   chr19 
                   3118795 
                   3119044 
                   0.620 
                   GNA11 
                 
                 
                     
                   chr19 
                   3118818 
                   3119047 
                   0.613 
                   GNA11 
                 
                 
                     
                   chr19 
                   3118863 
                   3119109 
                   0.636 
                   GNA11 
                 
                 
                     
                   chr19 
                   10600276 
                   10600491 
                   0.588 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10600284 
                   10600528 
                   0.592 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10600284 
                   10600532 
                   0.594 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10602242 
                   10602441 
                   0.645 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10602423 
                   10602671 
                   0.691 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10602539 
                   10602747 
                   0.632 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10602539 
                   10602753 
                   0.628 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10602653 
                   10602854 
                   0.609 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10610056 
                   10610289 
                   0.585 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10610069 
                   10610306 
                   0.576 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10610081 
                   10610306 
                   0.580 
                   KEAP1 
                 
                 
                     
                   chr19 
                   10610083 
                   10610306 
                   0.580 
                   KEAP1 
                 
                 
                     
                   chr19 
                   11094768 
                   11095038 
                   0.697 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11095950 
                   11096150 
                   0.592 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11096820 
                   11097078 
                   0.625 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11097475 
                   11097685 
                   0.645 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11098265 
                   11098553 
                   0.706 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11098298 
                   11098538 
                   0.726 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11098376 
                   11098606 
                   0.732 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11099901 
                   11100111 
                   0.607 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11101757 
                   11101957 
                   0.612 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11105466 
                   11105666 
                   0.522 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11106694 
                   11106939 
                   0.557 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11107143 
                   11107352 
                   0.476 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11113645 
                   11113845 
                   0.592 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11113855 
                   11114055 
                   0.493 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11118483 
                   11118683 
                   0.587 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11120977 
                   11121177 
                   0.557 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11123551 
                   11123751 
                   0.592 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11129571 
                   11129781 
                   0.555 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11130134 
                   11130372 
                   0.619 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11130167 
                   11130367 
                   0.612 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11130245 
                   11130468 
                   0.585 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11130248 
                   11130473 
                   0.584 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11132367 
                   11132587 
                   0.611 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11132607 
                   11132807 
                   0.622 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11134126 
                   11134326 
                   0.557 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11134905 
                   11135105 
                   0.617 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11135986 
                   11136186 
                   0.602 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11136874 
                   11137104 
                   0.610 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11138402 
                   11138674 
                   0.502 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11138598 
                   11138818 
                   0.597 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11141332 
                   11141532 
                   0.637 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11141549 
                   11141749 
                   0.627 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11143924 
                   11144134 
                   0.621 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11144041 
                   11144262 
                   0.617 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11144868 
                   11145108 
                   0.618 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11145552 
                   11145823 
                   0.654 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11151919 
                   11152129 
                   0.616 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11151919 
                   11152189 
                   0.627 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11152171 
                   11152371 
                   0.572 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11168890 
                   11169140 
                   0.625 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11169359 
                   11169619 
                   0.644 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11170610 
                   11170850 
                   0.668 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11172452 
                   11172706 
                   0.498 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11172557 
                   11172757 
                   0.423 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   11172753 
                   11172953 
                   0.493 
                   SMARCA4 
                 
                 
                     
                   chr19 
                   45854611 
                   45854870 
                   0.581 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45854917 
                   45855123 
                   0.589 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45855406 
                   45855649 
                   0.656 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45855711 
                   45855931 
                   0.611 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45855908 
                   45856123 
                   0.611 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45855910 
                   45856123 
                   0.612 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45855914 
                   45856123 
                   0.610 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45855948 
                   45856167 
                   0.609 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45855959 
                   45856169 
                   0.607 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45856222 
                   45856442 
                   0.652 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45857893 
                   45858113 
                   0.597 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45860528 
                   45860730 
                   0.635 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45860797 
                   45861007 
                   0.635 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45864772 
                   45864905 
                   0.575 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45866937 
                   45867137 
                   0.706 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45867119 
                   45867343 
                   0.724 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45867124 
                   45867373 
                   0.716 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45867329 
                   45867584 
                   0.684 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45867491 
                   45867711 
                   0.656 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45867506 
                   45867746 
                   0.660 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45867566 
                   45867806 
                   0.618 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45868096 
                   45868344 
                   0.635 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45868149 
                   45868349 
                   0.637 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45868154 
                   45868396 
                   0.626 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45868287 
                   45868486 
                   0.600 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45871786 
                   45871991 
                   0.524 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45872064 
                   45872264 
                   0.582 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45872211 
                   45872411 
                   0.562 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45873397 
                   45873585 
                   0.661 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45873421 
                   45873651 
                   0.675 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45873436 
                   45873665 
                   0.687 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45873632 
                   45873861 
                   0.700 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45873636 
                   45873901 
                   0.684 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45873726 
                   45873936 
                   0.645 
                   ERCC2 
                 
                 
                     
                   chr19 
                   45916987 
                   45917191 
                   0.571 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45918047 
                   45918240 
                   0.619 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45918047 
                   45918243 
                   0.619 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45918048 
                   45918243 
                   0.622 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45918053 
                   45918243 
                   0.628 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45918060 
                   45918235 
                   0.625 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45922222 
                   45922436 
                   0.567 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45923506 
                   45923678 
                   0.607 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45924445 
                   45924632 
                   0.638 
                   ERCC1 
                 
                 
                     
                   chr19 
                   45926611 
                   45926815 
                   0.615 
                   ERCC1 
                 
                 
                     
                   chr19 
                   50902097 
                   50902336 
                   0.650 
                   POLD1 
                 
                 
                     
                   chr19 
                   50902458 
                   50902658 
                   0.582 
                   POLD1 
                 
                 
                     
                   chr19 
                   50904960 
                   50905171 
                   0.656 
                   POLD1 
                 
                 
                     
                   chr19 
                   50905153 
                   50905392 
                   0.671 
                   POLD1 
                 
                 
                     
                   chr19 
                   50905436 
                   50905665 
                   0.683 
                   POLD1 
                 
                 
                     
                   chr19 
                   50905615 
                   50905913 
                   0.659 
                   POLD1 
                 
                 
                     
                   chr19 
                   50905899 
                   50906137 
                   0.665 
                   POLD1 
                 
                 
                     
                   chr19 
                   50906253 
                   50906464 
                   0.679 
                   POLD1 
                 
                 
                     
                   chr19 
                   50906723 
                   50906971 
                   0.622 
                   POLD1 
                 
                 
                     
                   chr19 
                   50906755 
                   50906971 
                   0.613 
                   POLD1 
                 
                 
                     
                   chr19 
                   50909485 
                   50909773 
                   0.640 
                   POLD1 
                 
                 
                     
                   chr19 
                   50910320 
                   50910533 
                   0.631 
                   POLD1 
                 
                 
                     
                   chr19 
                   50910334 
                   50910578 
                   0.629 
                   POLD1 
                 
                 
                     
                   chr19 
                   50910376 
                   50910627 
                   0.631 
                   POLD1 
                 
                 
                     
                   chr19 
                   50912042 
                   50912281 
                   0.617 
                   POLD1 
                 
                 
                     
                   chr19 
                   50912288 
                   50912520 
                   0.635 
                   POLD1 
                 
                 
                     
                   chr19 
                   50912795 
                   50913010 
                   0.667 
                   POLD1 
                 
                 
                     
                   chr19 
                   50916709 
                   50916950 
                   0.640 
                   POLD1 
                 
                 
                     
                   chr19 
                   50916970 
                   50917221 
                   0.623 
                   POLD1 
                 
                 
                     
                   chr19 
                   50917955 
                   50918169 
                   0.628 
                   POLD1 
                 
                 
                     
                   chr19 
                   50917960 
                   50918169 
                   0.624 
                   POLD1 
                 
                 
                     
                   chr19 
                   50918653 
                   50918824 
                   0.640 
                   POLD1 
                 
                 
                     
                   chr19 
                   50919033 
                   50919269 
                   0.692 
                   POLD1 
                 
                 
                     
                   chr19 
                   50919496 
                   50919745 
                   0.684 
                   POLD1 
                 
                 
                     
                   chr19 
                   50919683 
                   50919957 
                   0.691 
                   POLD1 
                 
                 
                     
                   chr19 
                   50919685 
                   50919957 
                   0.689 
                   POLD1 
                 
                 
                     
                   chr19 
                   50919770 
                   50920048 
                   0.699 
                   POLD1 
                 
                 
                     
                   chr19 
                   50919821 
                   50920050 
                   0.691 
                   POLD1 
                 
                 
                     
                   chr19 
                   50921104 
                   50921313 
                   0.576 
                   POLD1 
                 
                 
                     
                   chr2 
                   29443543 
                   29443787 
                   0.539 
                   ALK 
                 
                 
                     
                   chr2 
                   29443549 
                   29443783 
                   0.545 
                   ALK 
                 
                 
                     
                   chr2 
                   29443555 
                   29443789 
                   0.540 
                   ALK 
                 
                 
                     
                   chr2 
                   29443585 
                   29443816 
                   0.500 
                   ALK 
                 
                 
                     
                   chr2 
                   29445100 
                   29445340 
                   0.552 
                   ALK 
                 
                 
                     
                   chr2 
                   29445107 
                   29445340 
                   0.556 
                   ALK 
                 
                 
                     
                   chr2 
                   29445121 
                   29445350 
                   0.570 
                   ALK 
                 
                 
                     
                   chr2 
                   29445121 
                   29445367 
                   0.571 
                   ALK 
                 
                 
                     
                   chr2 
                   47600500 
                   47600700 
                   0.323 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47600912 
                   47601112 
                   0.473 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47601122 
                   47601322 
                   0.383 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47602199 
                   47602445 
                   0.328 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47604131 
                   47604282 
                   0.342 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47605987 
                   47606187 
                   0.249 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47606812 
                   47606991 
                   0.361 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47612268 
                   47612488 
                   0.398 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47613710 
                   47613910 
                   0.343 
                   EPCAM 
                 
                 
                     
                   chr2 
                   47630105 
                   47630305 
                   0.652 
                   MSH2 
                 
                 
                     
                   chr2 
                   47630152 
                   47630400 
                   0.643 
                   MSH2 
                 
                 
                     
                   chr2 
                   47630268 
                   47630467 
                   0.615 
                   MSH2 
                 
                 
                     
                   chr2 
                   47630315 
                   47630515 
                   0.667 
                   MSH2 
                 
                 
                     
                   chr2 
                   47630316 
                   47630530 
                   0.647 
                   MSH2 
                 
                 
                     
                   chr2 
                   47630384 
                   47630615 
                   0.690 
                   MSH2 
                 
                 
                     
                   chr2 
                   47630425 
                   47630625 
                   0.706 
                   MSH2 
                 
                 
                     
                   chr2 
                   47635539 
                   47635709 
                   0.339 
                   MSH2 
                 
                 
                     
                   chr2 
                   47637342 
                   47637582 
                   0.456 
                   MSH2 
                 
                 
                     
                   chr2 
                   47637389 
                   47637594 
                   0.442 
                   MSH2 
                 
                 
                     
                   chr2 
                   47639447 
                   47639662 
                   0.310 
                   MSH2 
                 
                 
                     
                   chr2 
                   47641283 
                   47641487 
                   0.327 
                   MSH2 
                 
                 
                     
                   chr2 
                   47643346 
                   47643546 
                   0.398 
                   MSH2 
                 
                 
                     
                   chr2 
                   47656945 
                   47657096 
                   0.388 
                   MSH2 
                 
                 
                     
                   chr2 
                   47672586 
                   47672786 
                   0.299 
                   MSH2 
                 
                 
                     
                   chr2 
                   47690076 
                   47690276 
                   0.303 
                   MSH2 
                 
                 
                     
                   chr2 
                   47693747 
                   47693947 
                   0.348 
                   MSH2 
                 
                 
                     
                   chr2 
                   47698159 
                   47698397 
                   0.326 
                   MSH2 
                 
                 
                     
                   chr2 
                   47702121 
                   47702341 
                   0.394 
                   MSH2 
                 
                 
                     
                   chr2 
                   47702174 
                   47702413 
                   0.388 
                   MSH2 
                 
                 
                     
                   chr2 
                   47703453 
                   47703653 
                   0.428 
                   MSH2 
                 
                 
                     
                   chr2 
                   47703663 
                   47703863 
                   0.363 
                   MSH2 
                 
                 
                     
                   chr2 
                   47705399 
                   47705630 
                   0.397 
                   MSH2 
                 
                 
                     
                   chr2 
                   47707788 
                   47708018 
                   0.424 
                   MSH2 
                 
                 
                     
                   chr2 
                   47709903 
                   47710113 
                   0.327 
                   MSH2 
                 
                 
                     
                   chr2 
                   47710107 
                   47710336 
                   0.287 
                   MSH2 
                 
                 
                     
                   chr2 
                   48010393 
                   48010592 
                   0.725 
                   MSH6 
                 
                 
                     
                   chr2 
                   48010420 
                   48010619 
                   0.740 
                   MSH6 
                 
                 
                     
                   chr2 
                   48010573 
                   48010824 
                   0.690 
                   MSH6 
                 
                 
                     
                   chr2 
                   48010575 
                   48010781 
                   0.725 
                   MSH6 
                 
                 
                     
                   chr2 
                   48017953 
                   48018200 
                   0.419 
                   MSH6 
                 
                 
                     
                   chr2 
                   48018205 
                   48018415 
                   0.431 
                   MSH6 
                 
                 
                     
                   chr2 
                   48023040 
                   48023272 
                   0.455 
                   MSH6 
                 
                 
                     
                   chr2 
                   48023105 
                   48023304 
                   0.430 
                   MSH6 
                 
                 
                     
                   chr2 
                   48025749 
                   48025949 
                   0.428 
                   MSH6 
                 
                 
                     
                   chr2 
                   48025933 
                   48026201 
                   0.476 
                   MSH6 
                 
                 
                     
                   chr2 
                   48026177 
                   48026376 
                   0.460 
                   MSH6 
                 
                 
                     
                   chr2 
                   48026340 
                   48026558 
                   0.457 
                   MSH6 
                 
                 
                     
                   chr2 
                   48026511 
                   48026711 
                   0.458 
                   MSH6 
                 
                 
                     
                   chr2 
                   48026765 
                   48026965 
                   0.383 
                   MSH6 
                 
                 
                     
                   chr2 
                   48027019 
                   48027219 
                   0.438 
                   MSH6 
                 
                 
                     
                   chr2 
                   48027273 
                   48027473 
                   0.438 
                   MSH6 
                 
                 
                     
                   chr2 
                   48027527 
                   48027727 
                   0.398 
                   MSH6 
                 
                 
                     
                   chr2 
                   48027746 
                   48028017 
                   0.426 
                   MSH6 
                 
                 
                     
                   chr2 
                   48028124 
                   48028364 
                   0.415 
                   MSH6 
                 
                 
                     
                   chr2 
                   48030536 
                   48030736 
                   0.433 
                   MSH6 
                 
                 
                     
                   chr2 
                   48030729 
                   48031008 
                   0.371 
                   MSH6 
                 
                 
                     
                   chr2 
                   48031952 
                   48032152 
                   0.443 
                   MSH6 
                 
                 
                     
                   chr2 
                   48032026 
                   48032237 
                   0.420 
                   MSH6 
                 
                 
                     
                   chr2 
                   48032772 
                   48032971 
                   0.315 
                   MSH6 
                 
                 
                     
                   chr2 
                   48033358 
                   48033554 
                   0.365 
                   MSH6 
                 
                 
                     
                   chr2 
                   48033416 
                   48033655 
                   0.367 
                   MSH6 
                 
                 
                     
                   chr2 
                   48033581 
                   48033782 
                   0.401 
                   MSH6 
                 
                 
                     
                   chr2 
                   48034024 
                   48034264 
                   0.307 
                   MSH6 
                 
                 
                     
                   chr2 
                   58386432 
                   58386632 
                   0.333 
                   FANCL 
                 
                 
                     
                   chr2 
                   58386777 
                   58386929 
                   0.307 
                   FANCL 
                 
                 
                     
                   chr2 
                   58387189 
                   58387389 
                   0.338 
                   FANCL 
                 
                 
                     
                   chr2 
                   58388496 
                   58388732 
                   0.346 
                   FANCL 
                 
                 
                     
                   chr2 
                   58389905 
                   58390169 
                   0.328 
                   FANCL 
                 
                 
                     
                   chr2 
                   58390005 
                   58390214 
                   0.352 
                   FANCL 
                 
                 
                     
                   chr2 
                   58390571 
                   58390773 
                   0.379 
                   FANCL 
                 
                 
                     
                   chr2 
                   58392779 
                   58392979 
                   0.398 
                   FANCL 
                 
                 
                     
                   chr2 
                   58431158 
                   58431358 
                   0.363 
                   FANCL 
                 
                 
                     
                   chr2 
                   58448972 
                   58449172 
                   0.323 
                   FANCL 
                 
                 
                     
                   chr2 
                   58453736 
                   58453936 
                   0.308 
                   FANCL 
                 
                 
                     
                   chr2 
                   58456824 
                   58457044 
                   0.285 
                   FANCL 
                 
                 
                     
                   chr2 
                   58459138 
                   58459342 
                   0.351 
                   FANCL 
                 
                 
                     
                   chr2 
                   58468279 
                   58468479 
                   0.592 
                   FANCL 
                 
                 
                     
                   chr2 
                   128014784 
                   128015047 
                   0.394 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128015087 
                   128015289 
                   0.522 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128016793 
                   128017023 
                   0.541 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128018729 
                   128018934 
                   0.476 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128028846 
                   128029046 
                   0.493 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128030334 
                   128030534 
                   0.488 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128036695 
                   128036895 
                   0.413 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128037952 
                   128038168 
                   0.535 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128044271 
                   128044501 
                   0.580 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128044494 
                   128044693 
                   0.500 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128046183 
                   128046383 
                   0.502 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128046840 
                   128047040 
                   0.468 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128047177 
                   128047377 
                   0.522 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128047669 
                   128047869 
                   0.448 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128050206 
                   128050419 
                   0.514 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128051102 
                   128051343 
                   0.566 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128051633 
                   128051852 
                   0.655 
                   ERCC3 
                 
                 
                     
                   chr2 
                   128051746 
                   128051946 
                   0.577 
                   ERCC3 
                 
                 
                     
                   chr2 
                   209112977 
                   209113230 
                   0.394 
                   IDH1 
                 
                 
                     
                   chr2 
                   209113091 
                   209113340 
                   0.444 
                   IDH1 
                 
                 
                     
                   chr2 
                   212288833 
                   212289075 
                   0.366 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212288836 
                   212289075 
                   0.367 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212288849 
                   212289089 
                   0.378 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212288867 
                   212289111 
                   0.376 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212483732 
                   212483976 
                   0.327 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212483745 
                   212483975 
                   0.338 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212483745 
                   212483989 
                   0.343 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212483745 
                   212483992 
                   0.347 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212529983 
                   212530215 
                   0.468 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212529983 
                   212530219 
                   0.468 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212530006 
                   212530255 
                   0.444 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212530049 
                   212530293 
                   0.420 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212587102 
                   212587341 
                   0.379 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212587102 
                   212587342 
                   0.378 
                   ERBB4 
                 
                 
                     
                   chr2 
                   212587104 
                   212587343 
                   0.379 
                   ERBB4 
                 
                 
                     
                   chr2 
                   215591713 
                   215591913 
                   0.348 
                   BARD1 
                 
                 
                     
                   chr2 
                   215592049 
                   215592249 
                   0.313 
                   BARD1 
                 
                 
                     
                   chr2 
                   215592385 
                   215592585 
                   0.318 
                   BARD1 
                 
                 
                     
                   chr2 
                   215592721 
                   215592921 
                   0.284 
                   BARD1 
                 
                 
                     
                   chr2 
                   215593393 
                   215593593 
                   0.458 
                   BARD1 
                 
                 
                     
                   chr2 
                   215593464 
                   215593712 
                   0.482 
                   BARD1 
                 
                 
                     
                   chr2 
                   215595070 
                   215595319 
                   0.348 
                   BARD1 
                 
                 
                     
                   chr2 
                   215609774 
                   215610018 
                   0.331 
                   BARD1 
                 
                 
                     
                   chr2 
                   215610357 
                   215610557 
                   0.368 
                   BARD1 
                 
                 
                     
                   chr2 
                   215617201 
                   215617402 
                   0.322 
                   BARD1 
                 
                 
                     
                   chr2 
                   215617244 
                   215617478 
                   0.315 
                   BARD1 
                 
                 
                     
                   chr2 
                   215632137 
                   215632347 
                   0.398 
                   BARD1 
                 
                 
                     
                   chr2 
                   215632347 
                   215632547 
                   0.299 
                   BARD1 
                 
                 
                     
                   chr2 
                   215633841 
                   215634041 
                   0.348 
                   BARD1 
                 
                 
                     
                   chr2 
                   215645283 
                   215645483 
                   0.418 
                   BARD1 
                 
                 
                     
                   chr2 
                   215645568 
                   215645768 
                   0.398 
                   BARD1 
                 
                 
                     
                   chr2 
                   215645789 
                   215646022 
                   0.385 
                   BARD1 
                 
                 
                     
                   chr2 
                   215645997 
                   215646196 
                   0.405 
                   BARD1 
                 
                 
                     
                   chr2 
                   215646018 
                   215646167 
                   0.413 
                   BARD1 
                 
                 
                     
                   chr2 
                   215656994 
                   215657164 
                   0.421 
                   BARD1 
                 
                 
                     
                   chr2 
                   215661815 
                   215662059 
                   0.355 
                   BARD1 
                 
                 
                     
                   chr2 
                   215674040 
                   215674299 
                   0.662 
                   BARD1 
                 
                 
                     
                   chr2 
                   215674057 
                   215674299 
                   0.671 
                   BARD1 
                 
                 
                     
                   chr2 
                   215674060 
                   215674299 
                   0.675 
                   BARD1 
                 
                 
                     
                   chr2 
                   215674115 
                   215674321 
                   0.681 
                   BARD1 
                 
                 
                     
                   chr20 
                   57484302 
                   57484538 
                   0.439 
                   GNAS 
                 
                 
                     
                   chr21 
                   36252718 
                   36252963 
                   0.427 
                   RUNX1 
                 
                 
                     
                   chr21 
                   36252753 
                   36253001 
                   0.454 
                   RUNX1 
                 
                 
                     
                   chr21 
                   36252796 
                   36253037 
                   0.471 
                   RUNX1 
                 
                 
                     
                   chr21 
                   36252819 
                   36253063 
                   0.469 
                   RUNX1 
                 
                 
                     
                   chr22 
                   29092793 
                   29093014 
                   0.383 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29095766 
                   29095985 
                   0.468 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29099378 
                   29099614 
                   0.354 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29105946 
                   29106126 
                   0.243 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29105988 
                   29106140 
                   0.288 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29107796 
                   29107996 
                   0.373 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29115374 
                   29115613 
                   0.292 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29120968 
                   29121207 
                   0.358 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29121185 
                   29121429 
                   0.376 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29130538 
                   29130762 
                   0.556 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29130552 
                   29130805 
                   0.508 
                   CHEK2 
                 
                 
                     
                   chr22 
                   29137634 
                   29137834 
                   0.547 
                   CHEK2 
                 
                 
                     
                   chr3 
                   10070202 
                   10070402 
                   0.383 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10074431 
                   10074641 
                   0.303 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10076444 
                   10076673 
                   0.430 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10076732 
                   10076932 
                   0.323 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10077981 
                   10078130 
                   0.313 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10080961 
                   10081110 
                   0.367 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10081391 
                   10081592 
                   0.510 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10083255 
                   10083471 
                   0.433 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10116194 
                   10116415 
                   0.405 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10119764 
                   10119916 
                   0.523 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10122693 
                   10122903 
                   0.422 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10122903 
                   10123103 
                   0.378 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10123144 
                   10123344 
                   0.358 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10127494 
                   10127703 
                   0.433 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10128659 
                   10128873 
                   0.414 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10130055 
                   10130255 
                   0.448 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10130418 
                   10130618 
                   0.398 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10131860 
                   10132052 
                   0.461 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10133776 
                   10133976 
                   0.418 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10134833 
                   10135033 
                   0.448 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10135971 
                   10136220 
                   0.484 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10136796 
                   10137016 
                   0.425 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10137928 
                   10138128 
                   0.398 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10140403 
                   10140603 
                   0.448 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10140685 
                   10140895 
                   0.322 
                   FANCD2 
                 
                 
                     
                   chr3 
                   10183302 
                   10183451 
                   0.653 
                   VHL 
                 
                 
                     
                   chr3 
                   10183681 
                   10183874 
                   0.706 
                   VHL 
                 
                 
                     
                   chr3 
                   10188234 
                   10188438 
                   0.390 
                   VHL 
                 
                 
                     
                   chr3 
                   10191445 
                   10191700 
                   0.484 
                   VHL 
                 
                 
                     
                   chr3 
                   10191721 
                   10191932 
                   0.392 
                   VHL 
                 
                 
                     
                   chr3 
                   10192245 
                   10192450 
                   0.350 
                   VHL 
                 
                 
                     
                   chr3 
                   12645599 
                   12645838 
                   0.504 
                   RAF1 
                 
                 
                     
                   chr3 
                   12645599 
                   12645843 
                   0.502 
                   RAF1 
                 
                 
                     
                   chr3 
                   12645599 
                   12645844 
                   0.500 
                   RAF1 
                 
                 
                     
                   chr3 
                   12645603 
                   12645844 
                   0.504 
                   RAF1 
                 
                 
                     
                   chr3 
                   14186692 
                   14186898 
                   0.319 
                   XPC 
                 
                 
                     
                   chr3 
                   14186863 
                   14187104 
                   0.521 
                   XPC 
                 
                 
                     
                   chr3 
                   14187085 
                   14187334 
                   0.532 
                   XPC 
                 
                 
                     
                   chr3 
                   14187312 
                   14187552 
                   0.589 
                   XPC 
                 
                 
                     
                   chr3 
                   14187523 
                   14187722 
                   0.570 
                   XPC 
                 
                 
                     
                   chr3 
                   14188679 
                   14188879 
                   0.552 
                   XPC 
                 
                 
                     
                   chr3 
                   14189299 
                   14189509 
                   0.583 
                   XPC 
                 
                 
                     
                   chr3 
                   14189991 
                   14190191 
                   0.597 
                   XPC 
                 
                 
                     
                   chr3 
                   14190286 
                   14190496 
                   0.578 
                   XPC 
                 
                 
                     
                   chr3 
                   14193741 
                   14194025 
                   0.596 
                   XPC 
                 
                 
                     
                   chr3 
                   14197850 
                   14198050 
                   0.483 
                   XPC 
                 
                 
                     
                   chr3 
                   14199573 
                   14199852 
                   0.543 
                   XPC 
                 
                 
                     
                   chr3 
                   14199862 
                   14200062 
                   0.582 
                   XPC 
                 
                 
                     
                   chr3 
                   14200146 
                   14200394 
                   0.522 
                   XPC 
                 
                 
                     
                   chr3 
                   14206322 
                   14206487 
                   0.434 
                   XPC 
                 
                 
                     
                   chr3 
                   14206933 
                   14207089 
                   0.522 
                   XPC 
                 
                 
                     
                   chr3 
                   14208699 
                   14208911 
                   0.474 
                   XPC 
                 
                 
                     
                   chr3 
                   14209663 
                   14209863 
                   0.517 
                   XPC 
                 
                 
                     
                   chr3 
                   14211839 
                   14212049 
                   0.384 
                   XPC 
                 
                 
                     
                   chr3 
                   14214355 
                   14214600 
                   0.476 
                   XPC 
                 
                 
                     
                   chr3 
                   14220004 
                   14220204 
                   0.682 
                   XPC 
                 
                 
                     
                   chr3 
                   37034589 
                   37034809 
                   0.570 
                   EPM2AIP1 
                 
                 
                     
                   chr3 
                   37034790 
                   37035063 
                   0.544 
                   EPM2AIP1 
                 
                 
                     
                   chr3 
                   37035069 
                   37035306 
                   0.622 
                   MLH1 
                 
                 
                     
                   chr3 
                   37038000 
                   37038200 
                   0.368 
                   MLH1 
                 
                 
                     
                   chr3 
                   37042434 
                   37042645 
                   0.354 
                   MLH1 
                 
                 
                     
                   chr3 
                   37045773 
                   37045973 
                   0.418 
                   MLH1 
                 
                 
                     
                   chr3 
                   37048411 
                   37048645 
                   0.353 
                   MLH1 
                 
                 
                     
                   chr3 
                   37050230 
                   37050436 
                   0.377 
                   MLH1 
                 
                 
                     
                   chr3 
                   37053207 
                   37053427 
                   0.335 
                   MLH1 
                 
                 
                     
                   chr3 
                   37053528 
                   37053730 
                   0.340 
                   MLH1 
                 
                 
                     
                   chr3 
                   37055893 
                   37056093 
                   0.373 
                   MLH1 
                 
                 
                     
                   chr3 
                   37058865 
                   37059114 
                   0.424 
                   MLH1 
                 
                 
                     
                   chr3 
                   37061804 
                   37062039 
                   0.542 
                   MLH1 
                 
                 
                     
                   chr3 
                   37067171 
                   37067392 
                   0.500 
                   MLH1 
                 
                 
                     
                   chr3 
                   37067236 
                   37067492 
                   0.514 
                   MLH1 
                 
                 
                     
                   chr3 
                   37070194 
                   37070394 
                   0.408 
                   MLH1 
                 
                 
                     
                   chr3 
                   37070355 
                   37070605 
                   0.462 
                   MLH1 
                 
                 
                     
                   chr3 
                   37081625 
                   37081777 
                   0.438 
                   MLH1 
                 
                 
                     
                   chr3 
                   37083681 
                   37083889 
                   0.354 
                   MLH1 
                 
                 
                     
                   chr3 
                   37088877 
                   37089113 
                   0.468 
                   MLH1 
                 
                 
                     
                   chr3 
                   37088933 
                   37089152 
                   0.473 
                   MLH1 
                 
                 
                     
                   chr3 
                   37089899 
                   37090099 
                   0.468 
                   MLH1 
                 
                 
                     
                   chr3 
                   37090327 
                   37090527 
                   0.428 
                   MLH1 
                 
                 
                     
                   chr3 
                   37091892 
                   37092087 
                   0.480 
                   MLH1 
                 
                 
                     
                   chr3 
                   37091894 
                   37092142 
                   0.466 
                   MLH1 
                 
                 
                     
                   chr3 
                   41265974 
                   41266223 
                   0.464 
                   CTNNB1 
                 
                 
                     
                   chr3 
                   41266013 
                   41266252 
                   0.488 
                   CTNNB1 
                 
                 
                     
                   chr3 
                   41266021 
                   41266268 
                   0.476 
                   CTNNB1 
                 
                 
                     
                   chr3 
                   41266036 
                   41266265 
                   0.474 
                   CTNNB1 
                 
                 
                     
                   chr3 
                   52435062 
                   52435320 
                   0.583 
                   BAP1 
                 
                 
                     
                   chr3 
                   52435350 
                   52435631 
                   0.543 
                   BAP1 
                 
                 
                     
                   chr3 
                   52435934 
                   52436211 
                   0.561 
                   BAP1 
                 
                 
                     
                   chr3 
                   52436217 
                   52436465 
                   0.647 
                   BAP1 
                 
                 
                     
                   chr3 
                   52436552 
                   52436790 
                   0.552 
                   BAP1 
                 
                 
                     
                   chr3 
                   52436807 
                   52437063 
                   0.572 
                   BAP1 
                 
                 
                     
                   chr3 
                   52437127 
                   52437370 
                   0.574 
                   BAP1 
                 
                 
                     
                   chr3 
                   52437447 
                   52437693 
                   0.599 
                   BAP1 
                 
                 
                     
                   chr3 
                   52437754 
                   52437978 
                   0.556 
                   BAP1 
                 
                 
                     
                   chr3 
                   52438443 
                   52438682 
                   0.575 
                   BAP1 
                 
                 
                     
                   chr3 
                   52439130 
                   52439357 
                   0.583 
                   BAP1 
                 
                 
                     
                   chr3 
                   52439752 
                   52440014 
                   0.544 
                   BAP1 
                 
                 
                     
                   chr3 
                   52440273 
                   52440505 
                   0.618 
                   BAP1 
                 
                 
                     
                   chr3 
                   52440695 
                   52440946 
                   0.552 
                   BAP1 
                 
                 
                     
                   chr3 
                   52441181 
                   52441475 
                   0.576 
                   BAP1 
                 
                 
                     
                   chr3 
                   52441983 
                   52442230 
                   0.532 
                   BAP1 
                 
                 
                     
                   chr3 
                   52442460 
                   52442693 
                   0.500 
                   BAP1 
                 
                 
                     
                   chr3 
                   52443505 
                   52443740 
                   0.602 
                   BAP1 
                 
                 
                     
                   chr3 
                   138374171 
                   138374400 
                   0.400 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138374183 
                   138374428 
                   0.386 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138374197 
                   138374427 
                   0.398 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138374204 
                   138374443 
                   0.408 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138409848 
                   138410087 
                   0.375 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138409848 
                   138410097 
                   0.380 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138409872 
                   138410116 
                   0.380 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138409872 
                   138410118 
                   0.385 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138417690 
                   138417920 
                   0.390 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138417690 
                   138417924 
                   0.383 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138417696 
                   138417915 
                   0.391 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138417697 
                   138417916 
                   0.395 
                   PIK3CB 
                 
                 
                     
                   chr3 
                   138665132 
                   138665361 
                   0.600 
                   FOXL2 
                 
                 
                     
                   chr3 
                   138665147 
                   138665396 
                   0.600 
                   FOXL2 
                 
                 
                     
                   chr3 
                   138665151 
                   138665396 
                   0.602 
                   FOXL2 
                 
                 
                     
                   chr3 
                   138665170 
                   138665409 
                   0.613 
                   FOXL2 
                 
                 
                     
                   chr3 
                   178916725 
                   178916970 
                   0.362 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178916766 
                   178917010 
                   0.351 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178916782 
                   178917028 
                   0.356 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178916822 
                   178917068 
                   0.336 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178917417 
                   178917566 
                   0.320 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178917417 
                   178917618 
                   0.347 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178917420 
                   178917590 
                   0.345 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178917420 
                   178917604 
                   0.351 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178921331 
                   178921578 
                   0.367 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178921339 
                   178921585 
                   0.372 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178921347 
                   178921596 
                   0.368 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178921364 
                   178921608 
                   0.351 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178927888 
                   178928114 
                   0.339 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178927898 
                   178928114 
                   0.346 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178927910 
                   178928144 
                   0.323 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178927974 
                   178928182 
                   0.354 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178935873 
                   178936102 
                   0.313 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178935930 
                   178936133 
                   0.353 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178935944 
                   178936197 
                   0.335 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178935995 
                   178936197 
                   0.365 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178936030 
                   178936279 
                   0.320 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178951914 
                   178952159 
                   0.382 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178951915 
                   178952140 
                   0.385 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178951921 
                   178952140 
                   0.386 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178951921 
                   178952159 
                   0.381 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178951948 
                   178952109 
                   0.389 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178952004 
                   178952152 
                   0.389 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178952010 
                   178952109 
                   0.390 
                   PIK3CA 
                 
                 
                     
                   chr3 
                   178952109 
                   178952152 
                   0.386 
                   PIK3CA 
                 
                 
                     
                   chr4 
                   55151865 
                   55152127 
                   0.513 
                   PDGFRA 
                 
                 
                     
                   chr4 
                   55593487 
                   55593733 
                   0.389 
                   KIT 
                 
                 
                     
                   chr4 
                   55593505 
                   55593749 
                   0.400 
                   KIT 
                 
                 
                     
                   chr4 
                   55593514 
                   55593765 
                   0.397 
                   KIT 
                 
                 
                     
                   chr4 
                   55593530 
                   55593778 
                   0.390 
                   KIT 
                 
                 
                     
                   chr4 
                   55594116 
                   55594365 
                   0.416 
                   KIT 
                 
                 
                     
                   chr4 
                   55594125 
                   55594365 
                   0.411 
                   KIT 
                 
                 
                     
                   chr4 
                   55594139 
                   55594380 
                   0.401 
                   KIT 
                 
                 
                     
                   chr4 
                   55594139 
                   55594385 
                   0.401 
                   KIT 
                 
                 
                     
                   chr4 
                   55599168 
                   55599408 
                   0.365 
                   KIT 
                 
                 
                     
                   chr4 
                   55599173 
                   55599417 
                   0.367 
                   KIT 
                 
                 
                     
                   chr4 
                   55599207 
                   55599435 
                   0.384 
                   KIT 
                 
                 
                     
                   chr4 
                   55602645 
                   55602892 
                   0.423 
                   KIT 
                 
                 
                     
                   chr4 
                   55602657 
                   55602888 
                   0.422 
                   KIT 
                 
                 
                     
                   chr4 
                   55602657 
                   55602892 
                   0.424 
                   KIT 
                 
                 
                     
                   chr4 
                   153244069 
                   153244316 
                   0.464 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153244075 
                   153244315 
                   0.465 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153244085 
                   153244324 
                   0.454 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153244106 
                   153244353 
                   0.427 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153245291 
                   153245531 
                   0.398 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153245297 
                   153245541 
                   0.400 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153245312 
                   153245560 
                   0.406 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153245328 
                   153245572 
                   0.396 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153247109 
                   153247353 
                   0.433 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153247122 
                   153247369 
                   0.448 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153247150 
                   153247399 
                   0.456 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153249264 
                   153249512 
                   0.414 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153249285 
                   153249525 
                   0.419 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153249290 
                   153249529 
                   0.417 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153249303 
                   153249551 
                   0.414 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153250763 
                   153251006 
                   0.340 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153250791 
                   153251017 
                   0.348 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153250791 
                   153251031 
                   0.349 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153250808 
                   153251047 
                   0.342 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153251774 
                   153252018 
                   0.380 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153251789 
                   153252028 
                   0.388 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153251792 
                   153252040 
                   0.382 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153251832 
                   153252071 
                   0.379 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153258843 
                   153259092 
                   0.356 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153258850 
                   153259097 
                   0.355 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153258888 
                   153259137 
                   0.344 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153258953 
                   153259199 
                   0.368 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153268077 
                   153268219 
                   0.517 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153268078 
                   153268219 
                   0.514 
                   FBXW7 
                 
                 
                     
                   chr4 
                   153268079 
                   153268219 
                   0.518 
                   FBXW7 
                 
                 
                     
                   chr5 
                   56161075 
                   56161306 
                   0.328 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56161096 
                   56161325 
                   0.330 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56161113 
                   56161321 
                   0.349 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56161178 
                   56161386 
                   0.321 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56161545 
                   56161787 
                   0.346 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56161548 
                   56161797 
                   0.348 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56161563 
                   56161807 
                   0.355 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56161577 
                   56161806 
                   0.365 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56180437 
                   56180676 
                   0.363 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56180457 
                   56180659 
                   0.389 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56180502 
                   56180707 
                   0.369 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56181614 
                   56181861 
                   0.335 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56181627 
                   56181876 
                   0.332 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56181632 
                   56181871 
                   0.338 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56181648 
                   56181887 
                   0.346 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56183135 
                   56183374 
                   0.429 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56183138 
                   56183347 
                   0.429 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56183138 
                   56183361 
                   0.429 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   56183176 
                   56183375 
                   0.455 
                   MAP3K1 
                 
                 
                     
                   chr5 
                   112043137 
                   112043364 
                   0.649 
                   APC 
                 
                 
                     
                   chr5 
                   112043137 
                   112043365 
                   0.651 
                   APC 
                 
                 
                     
                   chr5 
                   112043186 
                   112043431 
                   0.663 
                   APC 
                 
                 
                     
                   chr5 
                   112043190 
                   112043431 
                   0.661 
                   APC 
                 
                 
                     
                   chr5 
                   112043201 
                   112043471 
                   0.672 
                   APC 
                 
                 
                     
                   chr5 
                   112043206 
                   112043428 
                   0.668 
                   APC 
                 
                 
                     
                   chr5 
                   112073451 
                   112073699 
                   0.639 
                   APC 
                 
                 
                     
                   chr5 
                   112073948 
                   112074148 
                   0.488 
                   APC 
                 
                 
                     
                   chr5 
                   112090491 
                   112090691 
                   0.373 
                   APC 
                 
                 
                     
                   chr5 
                   112102006 
                   112102208 
                   0.330 
                   APC 
                 
                 
                     
                   chr5 
                   112102893 
                   112103093 
                   0.433 
                   APC 
                 
                 
                     
                   chr5 
                   112111368 
                   112111578 
                   0.289 
                   APC 
                 
                 
                     
                   chr5 
                   112116375 
                   112116639 
                   0.340 
                   APC 
                 
                 
                     
                   chr5 
                   112128134 
                   112128341 
                   0.332 
                   APC 
                 
                 
                     
                   chr5 
                   112128152 
                   112128420 
                   0.309 
                   APC 
                 
                 
                     
                   chr5 
                   112136780 
                   112137014 
                   0.404 
                   APC 
                 
                 
                     
                   chr5 
                   112151086 
                   112151286 
                   0.368 
                   APC 
                 
                 
                     
                   chr5 
                   112154610 
                   112154859 
                   0.424 
                   APC 
                 
                 
                     
                   chr5 
                   112154826 
                   112155071 
                   0.504 
                   APC 
                 
                 
                     
                   chr5 
                   112157485 
                   112157695 
                   0.341 
                   APC 
                 
                 
                     
                   chr5 
                   112162781 
                   112162991 
                   0.379 
                   APC 
                 
                 
                     
                   chr5 
                   112163441 
                   112163655 
                   0.288 
                   APC 
                 
                 
                     
                   chr5 
                   112163452 
                   112163681 
                   0.309 
                   APC 
                 
                 
                     
                   chr5 
                   112164471 
                   112164655 
                   0.319 
                   APC 
                 
                 
                     
                   chr5 
                   112170600 
                   112170800 
                   0.393 
                   APC 
                 
                 
                     
                   chr5 
                   112170810 
                   112171010 
                   0.289 
                   APC 
                 
                 
                     
                   chr5 
                   112173249 
                   112173449 
                   0.383 
                   APC 
                 
                 
                     
                   chr5 
                   112173471 
                   112173712 
                   0.405 
                   APC 
                 
                 
                     
                   chr5 
                   112173688 
                   112173932 
                   0.404 
                   APC 
                 
                 
                     
                   chr5 
                   112173840 
                   112174071 
                   0.466 
                   APC 
                 
                 
                     
                   chr5 
                   112174070 
                   112174313 
                   0.361 
                   APC 
                 
                 
                     
                   chr5 
                   112174297 
                   112174537 
                   0.353 
                   APC 
                 
                 
                     
                   chr5 
                   112174544 
                   112174783 
                   0.392 
                   APC 
                 
                 
                     
                   chr5 
                   112174788 
                   112175027 
                   0.400 
                   APC 
                 
                 
                     
                   chr5 
                   112174985 
                   112175185 
                   0.378 
                   APC 
                 
                 
                     
                   chr5 
                   112175164 
                   112175405 
                   0.459 
                   APC 
                 
                 
                     
                   chr5 
                   112175413 
                   112175652 
                   0.471 
                   APC 
                 
                 
                     
                   chr5 
                   112175519 
                   112175768 
                   0.460 
                   APC 
                 
                 
                     
                   chr5 
                   112175523 
                   112175780 
                   0.461 
                   APC 
                 
                 
                     
                   chr5 
                   112175853 
                   112176053 
                   0.333 
                   APC 
                 
                 
                     
                   chr5 
                   112175867 
                   112176116 
                   0.380 
                   APC 
                 
                 
                     
                   chr5 
                   112175900 
                   112176040 
                   0.326 
                   APC 
                 
                 
                     
                   chr5 
                   112176145 
                   112176391 
                   0.449 
                   APC 
                 
                 
                     
                   chr5 
                   112176384 
                   112176633 
                   0.412 
                   APC 
                 
                 
                     
                   chr5 
                   112176631 
                   112176875 
                   0.322 
                   APC 
                 
                 
                     
                   chr5 
                   112176860 
                   112177104 
                   0.396 
                   APC 
                 
                 
                     
                   chr5 
                   112176995 
                   112177234 
                   0.400 
                   APC 
                 
                 
                     
                   chr5 
                   112177404 
                   112177650 
                   0.385 
                   APC 
                 
                 
                     
                   chr5 
                   112177589 
                   112177789 
                   0.408 
                   APC 
                 
                 
                     
                   chr5 
                   112177796 
                   112178080 
                   0.389 
                   APC 
                 
                 
                     
                   chr5 
                   112178130 
                   112178379 
                   0.456 
                   APC 
                 
                 
                     
                   chr5 
                   112178293 
                   112178573 
                   0.391 
                   APC 
                 
                 
                     
                   chr5 
                   112178510 
                   112178755 
                   0.407 
                   APC 
                 
                 
                     
                   chr5 
                   112178763 
                   112179036 
                   0.449 
                   APC 
                 
                 
                     
                   chr5 
                   112179030 
                   112179324 
                   0.380 
                   APC 
                 
                 
                     
                   chr5 
                   112179325 
                   112179525 
                   0.423 
                   APC 
                 
                 
                     
                   chr5 
                   112179582 
                   112179827 
                   0.472 
                   APC 
                 
                 
                     
                   chr5 
                   112180193 
                   112180393 
                   0.338 
                   APC 
                 
                 
                     
                   chr5 
                   112181061 
                   112181261 
                   0.398 
                   APC 
                 
                 
                     
                   chr5 
                   112181929 
                   112182129 
                   0.313 
                   APC 
                 
                 
                     
                   chr5 
                   131892606 
                   131892857 
                   0.718 
                   RAD50 
                 
                 
                     
                   chr5 
                   131892983 
                   131893197 
                   0.474 
                   RAD50 
                 
                 
                     
                   chr5 
                   131892984 
                   131893223 
                   0.463 
                   RAD50 
                 
                 
                     
                   chr5 
                   131893020 
                   131893223 
                   0.466 
                   RAD50 
                 
                 
                     
                   chr5 
                   131893049 
                   131893292 
                   0.492 
                   RAD50 
                 
                 
                     
                   chr5 
                   131894808 
                   131895037 
                   0.252 
                   RAD50 
                 
                 
                     
                   chr5 
                   131911382 
                   131911618 
                   0.376 
                   RAD50 
                 
                 
                     
                   chr5 
                   131915004 
                   131915223 
                   0.382 
                   RAD50 
                 
                 
                     
                   chr5 
                   131915567 
                   131915717 
                   0.364 
                   RAD50 
                 
                 
                     
                   chr5 
                   131923251 
                   131923500 
                   0.312 
                   RAD50 
                 
                 
                     
                   chr5 
                   131923517 
                   131923757 
                   0.328 
                   RAD50 
                 
                 
                     
                   chr5 
                   131924402 
                   131924651 
                   0.364 
                   RAD50 
                 
                 
                     
                   chr5 
                   131925323 
                   131925552 
                   0.343 
                   RAD50 
                 
                 
                     
                   chr5 
                   131926850 
                   131927094 
                   0.363 
                   RAD50 
                 
                 
                     
                   chr5 
                   131927570 
                   131927750 
                   0.354 
                   RAD50 
                 
                 
                     
                   chr5 
                   131930491 
                   131930738 
                   0.323 
                   RAD50 
                 
                 
                     
                   chr5 
                   131931278 
                   131931508 
                   0.442 
                   RAD50 
                 
                 
                     
                   chr5 
                   131939061 
                   131939291 
                   0.377 
                   RAD50 
                 
                 
                     
                   chr5 
                   131939553 
                   131939789 
                   0.350 
                   RAD50 
                 
                 
                     
                   chr5 
                   131940409 
                   131940654 
                   0.346 
                   RAD50 
                 
                 
                     
                   chr5 
                   131944351 
                   131944557 
                   0.261 
                   RAD50 
                 
                 
                     
                   chr5 
                   131944387 
                   131944597 
                   0.251 
                   RAD50 
                 
                 
                     
                   chr5 
                   131944873 
                   131945090 
                   0.271 
                   RAD50 
                 
                 
                     
                   chr5 
                   131951603 
                   131951803 
                   0.323 
                   RAD50 
                 
                 
                     
                   chr5 
                   131951820 
                   131952020 
                   0.294 
                   RAD50 
                 
                 
                     
                   chr5 
                   131953730 
                   131953966 
                   0.333 
                   RAD50 
                 
                 
                     
                   chr5 
                   131972864 
                   131973090 
                   0.454 
                   RAD50 
                 
                 
                     
                   chr5 
                   131973728 
                   131973957 
                   0.443 
                   RAD50 
                 
                 
                     
                   chr5 
                   131976168 
                   131976417 
                   0.520 
                   RAD50 
                 
                 
                     
                   chr5 
                   131977815 
                   131978052 
                   0.378 
                   RAD50 
                 
                 
                     
                   chr5 
                   131978075 
                   131978308 
                   0.372 
                   RAD50 
                 
                 
                     
                   chr5 
                   131978265 
                   131978518 
                   0.417 
                   RAD50 
                 
                 
                     
                   chr5 
                   131978882 
                   131979101 
                   0.486 
                   RAD50 
                 
                 
                     
                   chr5 
                   170837389 
                   170837646 
                   0.318 
                   NPM1 
                 
                 
                     
                   chr5 
                   170837423 
                   170837672 
                   0.316 
                   NPM1 
                 
                 
                     
                   chr6 
                   35419950 
                   35420204 
                   0.710 
                   FANCE 
                 
                 
                     
                   chr6 
                   35420484 
                   35420712 
                   0.677 
                   FANCE 
                 
                 
                     
                   chr6 
                   35423523 
                   35423753 
                   0.610 
                   FANCE 
                 
                 
                     
                   chr6 
                   35423747 
                   35423980 
                   0.568 
                   FANCE 
                 
                 
                     
                   chr6 
                   35423937 
                   35424160 
                   0.500 
                   FANCE 
                 
                 
                     
                   chr6 
                   35425325 
                   35425579 
                   0.541 
                   FANCE 
                 
                 
                     
                   chr6 
                   35425576 
                   35425862 
                   0.516 
                   FANCE 
                 
                 
                     
                   chr6 
                   35425990 
                   35426190 
                   0.602 
                   FANCE 
                 
                 
                     
                   chr6 
                   35427014 
                   35427214 
                   0.443 
                   FANCE 
                 
                 
                     
                   chr6 
                   35427343 
                   35427543 
                   0.552 
                   FANCE 
                 
                 
                     
                   chr6 
                   35428293 
                   35428492 
                   0.560 
                   FANCE 
                 
                 
                     
                   chr6 
                   35433986 
                   35434203 
                   0.550 
                   FANCE 
                 
                 
                     
                   chr6 
                   35434173 
                   35434385 
                   0.493 
                   FANCE 
                 
                 
                     
                   chr6 
                   43544117 
                   43544321 
                   0.459 
                   POLH 
                 
                 
                     
                   chr6 
                   43550014 
                   43550163 
                   0.420 
                   POLH 
                 
                 
                     
                   chr6 
                   43550754 
                   43550953 
                   0.415 
                   POLH 
                 
                 
                     
                   chr6 
                   43554978 
                   43555223 
                   0.476 
                   POLH 
                 
                 
                     
                   chr6 
                   43565476 
                   43565625 
                   0.467 
                   POLH 
                 
                 
                     
                   chr6 
                   43568621 
                   43568821 
                   0.448 
                   POLH 
                 
                 
                     
                   chr6 
                   43571533 
                   43571733 
                   0.423 
                   POLH 
                 
                 
                     
                   chr6 
                   43572382 
                   43572582 
                   0.433 
                   POLH 
                 
                 
                     
                   chr6 
                   43572829 
                   43573058 
                   0.374 
                   POLH 
                 
                 
                     
                   chr6 
                   43578220 
                   43578420 
                   0.507 
                   POLH 
                 
                 
                     
                   chr6 
                   43581333 
                   43581514 
                   0.407 
                   POLH 
                 
                 
                     
                   chr6 
                   43581613 
                   43581843 
                   0.433 
                   POLH 
                 
                 
                     
                   chr6 
                   43581852 
                   43582085 
                   0.517 
                   POLH 
                 
                 
                     
                   chr6 
                   43582072 
                   43582231 
                   0.475 
                   POLH 
                 
                 
                     
                   chr6 
                   43587356 
                   43587593 
                   0.361 
                   POLH 
                 
                 
                     
                   chr6 
                   43587578 
                   43587778 
                   0.393 
                   POLH 
                 
                 
                     
                   chr6 
                   43587842 
                   43588084 
                   0.444 
                   POLH 
                 
                 
                     
                   chr6 
                   152265305 
                   152265551 
                   0.555 
                   ESR1 
                 
                 
                     
                   chr6 
                   152265322 
                   152265569 
                   0.556 
                   ESR1 
                 
                 
                     
                   chr6 
                   152265335 
                   152265582 
                   0.548 
                   ESR1 
                 
                 
                     
                   chr6 
                   152265349 
                   152265597 
                   0.562 
                   ESR1 
                 
                 
                     
                   chr6 
                   152332663 
                   152332910 
                   0.444 
                   ESR1 
                 
                 
                     
                   chr6 
                   152332707 
                   152332937 
                   0.463 
                   ESR1 
                 
                 
                     
                   chr6 
                   152332732 
                   152332961 
                   0.483 
                   ESR1 
                 
                 
                     
                   chr6 
                   152415449 
                   152415694 
                   0.553 
                   ESR1 
                 
                 
                     
                   chr6 
                   152415449 
                   152415729 
                   0.555 
                   ESR1 
                 
                 
                     
                   chr6 
                   152415452 
                   152415694 
                   0.556 
                   ESR1 
                 
                 
                     
                   chr6 
                   152415469 
                   152415763 
                   0.542 
                   ESR1 
                 
                 
                     
                   chr6 
                   152419792 
                   152420036 
                   0.576 
                   ESR1 
                 
                 
                     
                   chr6 
                   152419822 
                   152420047 
                   0.575 
                   ESR1 
                 
                 
                     
                   chr6 
                   152419877 
                   152420111 
                   0.591 
                   ESR1 
                 
                 
                     
                   chr7 
                   6029374 
                   6029583 
                   0.367 
                   PMS2 
                 
                 
                     
                   chr7 
                   6035119 
                   6035348 
                   0.387 
                   PMS2 
                 
                 
                     
                   chr7 
                   6036912 
                   6037112 
                   0.378 
                   PMS2 
                 
                 
                     
                   chr7 
                   6038718 
                   6039008 
                   0.430 
                   PMS2 
                 
                 
                     
                   chr7 
                   55241468 
                   55241710 
                   0.564 
                   EGFR 
                 
                 
                     
                   chr7 
                   55241542 
                   55241789 
                   0.565 
                   EGFR 
                 
                 
                     
                   chr7 
                   55241576 
                   55241746 
                   0.526 
                   EGFR 
                 
                 
                     
                   chr7 
                   55241613 
                   55241853 
                   0.531 
                   EGFR 
                 
                 
                     
                   chr7 
                   55242269 
                   55242500 
                   0.509 
                   EGFR 
                 
                 
                     
                   chr7 
                   55242271 
                   55242505 
                   0.506 
                   EGFR 
                 
                 
                     
                   chr7 
                   55242272 
                   55242520 
                   0.506 
                   EGFR 
                 
                 
                     
                   chr7 
                   55242280 
                   55242532 
                   0.506 
                   EGFR 
                 
                 
                     
                   chr7 
                   55242319 
                   55242558 
                   0.496 
                   EGFR 
                 
                 
                     
                   chr7 
                   55242332 
                   55242584 
                   0.490 
                   EGFR 
                 
                 
                     
                   chr7 
                   55248852 
                   55249080 
                   0.585 
                   EGFR 
                 
                 
                     
                   chr7 
                   55248896 
                   55249120 
                   0.622 
                   EGFR 
                 
                 
                     
                   chr7 
                   55248933 
                   55249182 
                   0.600 
                   EGFR 
                 
                 
                     
                   chr7 
                   55248937 
                   55249187 
                   0.598 
                   EGFR 
                 
                 
                     
                   chr7 
                   55248961 
                   55249208 
                   0.597 
                   EGFR 
                 
                 
                     
                   chr7 
                   55259335 
                   55259571 
                   0.523 
                   EGFR 
                 
                 
                     
                   chr7 
                   55259337 
                   55259586 
                   0.532 
                   EGFR 
                 
                 
                     
                   chr7 
                   55259356 
                   55259602 
                   0.534 
                   EGFR 
                 
                 
                     
                   chr7 
                   55259368 
                   55259570 
                   0.537 
                   EGFR 
                 
                 
                     
                   chr7 
                   55259391 
                   55259640 
                   0.544 
                   EGFR 
                 
                 
                     
                   chr7 
                   116411722 
                   116411963 
                   0.417 
                   MET 
                 
                 
                     
                   chr7 
                   116411832 
                   116412076 
                   0.424 
                   MET 
                 
                 
                     
                   chr7 
                   116411854 
                   116412102 
                   0.410 
                   MET 
                 
                 
                     
                   chr7 
                   116411942 
                   116412183 
                   0.347 
                   MET 
                 
                 
                     
                   chr7 
                   140453006 
                   140453257 
                   0.381 
                   BRAF 
                 
                 
                     
                   chr7 
                   140453042 
                   140453283 
                   0.364 
                   BRAF 
                 
                 
                     
                   chr7 
                   140453060 
                   140453259 
                   0.385 
                   BRAF 
                 
                 
                     
                   chr7 
                   140453085 
                   140453319 
                   0.336 
                   BRAF 
                 
                 
                     
                   chr7 
                   140453086 
                   140453335 
                   0.340 
                   BRAF 
                 
                 
                     
                   chr7 
                   140453105 
                   140453353 
                   0.329 
                   BRAF 
                 
                 
                     
                   chr7 
                   140481224 
                   140481471 
                   0.355 
                   BRAF 
                 
                 
                     
                   chr7 
                   140481234 
                   140481475 
                   0.360 
                   BRAF 
                 
                 
                     
                   chr7 
                   140481251 
                   140481496 
                   0.358 
                   BRAF 
                 
                 
                     
                   chr7 
                   140481263 
                   140481507 
                   0.363 
                   BRAF 
                 
                 
                     
                   chr8 
                   90947700 
                   90947947 
                   0.319 
                   NBN 
                 
                 
                     
                   chr8 
                   90949123 
                   90949343 
                   0.326 
                   NBN 
                 
                 
                     
                   chr8 
                   90955446 
                   90955690 
                   0.351 
                   NBN 
                 
                 
                     
                   chr8 
                   90958290 
                   90958510 
                   0.321 
                   NBN 
                 
                 
                     
                   chr8 
                   90959971 
                   90960119 
                   0.329 
                   NBN 
                 
                 
                     
                   chr8 
                   90965407 
                   90965703 
                   0.347 
                   NBN 
                 
                 
                     
                   chr8 
                   90965709 
                   90965960 
                   0.333 
                   NBN 
                 
                 
                     
                   chr8 
                   90967522 
                   90967722 
                   0.388 
                   NBN 
                 
                 
                     
                   chr8 
                   90967762 
                   90967962 
                   0.299 
                   NBN 
                 
                 
                     
                   chr8 
                   90970951 
                   90971177 
                   0.414 
                   NBN 
                 
                 
                     
                   chr8 
                   90976592 
                   90976816 
                   0.324 
                   NBN 
                 
                 
                     
                   chr8 
                   90976592 
                   90976817 
                   0.323 
                   NBN 
                 
                 
                     
                   chr8 
                   90982598 
                   90982805 
                   0.385 
                   NBN 
                 
                 
                     
                   chr8 
                   90983304 
                   90983514 
                   0.308 
                   NBN 
                 
                 
                     
                   chr8 
                   90990344 
                   90990544 
                   0.318 
                   NBN 
                 
                 
                     
                   chr8 
                   90992886 
                   90993086 
                   0.323 
                   NBN 
                 
                 
                     
                   chr8 
                   90993103 
                   90993303 
                   0.284 
                   NBN 
                 
                 
                     
                   chr8 
                   90993522 
                   90993742 
                   0.321 
                   NBN 
                 
                 
                     
                   chr8 
                   90994780 
                   90995004 
                   0.347 
                   NBN 
                 
                 
                     
                   chr8 
                   90996593 
                   90996859 
                   0.678 
                   NBN 
                 
                 
                     
                   chr9 
                   5073651 
                   5073873 
                   0.354 
                   JAK2 
                 
                 
                     
                   chr9 
                   21968200 
                   21968432 
                   0.545 
                   CDKN2A 
                 
                 
                     
                   chr9 
                   21970919 
                   21971216 
                   0.721 
                   CDKN2A 
                 
                 
                     
                   chr9 
                   21970920 
                   21971216 
                   0.721 
                   CDKN2A 
                 
                 
                     
                   chr9 
                   21973486 
                   21973718 
                   0.365 
                   CDKN2A 
                 
                 
                     
                   chr9 
                   21974363 
                   21974602 
                   0.500 
                   CDKN2A 
                 
                 
                     
                   chr9 
                   21994083 
                   21994336 
                   0.654 
                   CDKN2A 
                 
                 
                     
                   chr9 
                   21994085 
                   21994334 
                   0.656 
                   CDKN2A 
                 
                 
                     
                   chr9 
                   35073773 
                   35074045 
                   0.432 
                   FANCG 
                 
                 
                     
                   chr9 
                   35074052 
                   35074258 
                   0.517 
                   FANCG 
                 
                 
                     
                   chr9 
                   35074248 
                   35074484 
                   0.565 
                   FANCG 
                 
                 
                     
                   chr9 
                   35074847 
                   35075072 
                   0.535 
                   FANCG 
                 
                 
                     
                   chr9 
                   35075125 
                   35075335 
                   0.493 
                   FANCG 
                 
                 
                     
                   chr9 
                   35075354 
                   35075564 
                   0.531 
                   FANCG 
                 
                 
                     
                   chr9 
                   35075451 
                   35075651 
                   0.562 
                   FANCG 
                 
                 
                     
                   chr9 
                   35075668 
                   35075868 
                   0.587 
                   FANCG 
                 
                 
                     
                   chr9 
                   35075897 
                   35076097 
                   0.557 
                   FANCG 
                 
                 
                     
                   chr9 
                   35076388 
                   35076632 
                   0.494 
                   FANCG 
                 
                 
                     
                   chr9 
                   35076699 
                   35076959 
                   0.529 
                   FANCG 
                 
                 
                     
                   chr9 
                   35076908 
                   35077108 
                   0.537 
                   FANCG 
                 
                 
                     
                   chr9 
                   35077204 
                   35077404 
                   0.517 
                   FANCG 
                 
                 
                     
                   chr9 
                   35078145 
                   35078385 
                   0.593 
                   FANCG 
                 
                 
                     
                   chr9 
                   35078512 
                   35078712 
                   0.522 
                   FANCG 
                 
                 
                     
                   chr9 
                   35079068 
                   35079268 
                   0.587 
                   FANCG 
                 
                 
                     
                   chr9 
                   35079437 
                   35079667 
                   0.671 
                   FANCG 
                 
                 
                     
                   chr9 
                   35079767 
                   35079970 
                   0.667 
                   FANCG 
                 
                 
                     
                   chr9 
                   35079828 
                   35080069 
                   0.702 
                   FANCG 
                 
                 
                     
                   chr9 
                   35079839 
                   35080069 
                   0.706 
                   FANCG 
                 
                 
                     
                   chr9 
                   35079923 
                   35080159 
                   0.667 
                   FANCG 
                 
                 
                     
                   chr9 
                   80336120 
                   80336372 
                   0.478 
                   GNAQ 
                 
                 
                     
                   chr9 
                   80336121 
                   80336372 
                   0.476 
                   GNAQ 
                 
                 
                     
                   chr9 
                   80336223 
                   80336472 
                   0.500 
                   GNAQ 
                 
                 
                     
                   chr9 
                   80336253 
                   80336500 
                   0.484 
                   GNAQ 
                 
                 
                     
                   chr9 
                   80336259 
                   80336500 
                   0.483 
                   GNAQ 
                 
                 
                     
                   chr9 
                   80409367 
                   80409598 
                   0.353 
                   GNAQ 
                 
                 
                     
                   chr9 
                   80409379 
                   80409628 
                   0.352 
                   GNAQ 
                 
                 
                     
                   chr9 
                   97863312 
                   97863512 
                   0.572 
                   FANCC 
                 
                 
                     
                   chr9 
                   97863840 
                   97864111 
                   0.548 
                   FANCC 
                 
                 
                     
                   chr9 
                   97869338 
                   97869594 
                   0.595 
                   FANCC 
                 
                 
                     
                   chr9 
                   97872619 
                   97872829 
                   0.308 
                   FANCC 
                 
                 
                     
                   chr9 
                   97872955 
                   97873165 
                   0.398 
                   FANCC 
                 
                 
                     
                   chr9 
                   97873179 
                   97873409 
                   0.494 
                   FANCC 
                 
                 
                     
                   chr9 
                   97873711 
                   97873957 
                   0.587 
                   FANCC 
                 
                 
                     
                   chr9 
                   97876827 
                   97877027 
                   0.517 
                   FANCC 
                 
                 
                     
                   chr9 
                   97879613 
                   97879852 
                   0.404 
                   FANCC 
                 
                 
                     
                   chr9 
                   97887262 
                   97887462 
                   0.403 
                   FANCC 
                 
                 
                     
                   chr9 
                   97888682 
                   97888882 
                   0.423 
                   FANCC 
                 
                 
                     
                   chr9 
                   97897551 
                   97897761 
                   0.417 
                   FANCC 
                 
                 
                     
                   chr9 
                   97897761 
                   97897961 
                   0.313 
                   FANCC 
                 
                 
                     
                   chr9 
                   97912208 
                   97912455 
                   0.456 
                   FANCC 
                 
                 
                     
                   chr9 
                   97933298 
                   97933498 
                   0.363 
                   FANCC 
                 
                 
                     
                   chr9 
                   97934219 
                   97934419 
                   0.333 
                   FANCC 
                 
                 
                     
                   chr9 
                   98002823 
                   98003043 
                   0.321 
                   FANCC 
                 
                 
                     
                   chr9 
                   98009694 
                   98009940 
                   0.328 
                   FANCC 
                 
                 
                     
                   chr9 
                   98011375 
                   98011575 
                   0.418 
                   FANCC 
                 
                 
                     
                   chr9 
                   98011585 
                   98011785 
                   0.433 
                   FANCC 
                 
                 
                     
                   chr9 
                   98079868 
                   98080148 
                   0.669 
                   FANCC 
                 
                 
                     
                   chr9 
                   100437190 
                   100437390 
                   0.428 
                   XPA 
                 
                 
                     
                   chr9 
                   100437359 
                   100437558 
                   0.475 
                   XPA 
                 
                 
                     
                   chr9 
                   100437525 
                   100437765 
                   0.299 
                   XPA 
                 
                 
                     
                   chr9 
                   100437793 
                   100437993 
                   0.383 
                   XPA 
                 
                 
                     
                   chr9 
                   100444474 
                   100444677 
                   0.397 
                   XPA 
                 
                 
                     
                   chr9 
                   100447108 
                   100447308 
                   0.348 
                   XPA 
                 
                 
                     
                   chr9 
                   100449321 
                   100449540 
                   0.309 
                   XPA 
                 
                 
                     
                   chr9 
                   100451744 
                   100451944 
                   0.323 
                   XPA 
                 
                 
                     
                   chr9 
                   100455831 
                   100456031 
                   0.328 
                   XPA 
                 
                 
                     
                   chr9 
                   100459275 
                   100459499 
                   0.720 
                   XPA 
                 
                 
                     
                   chr9 
                   100459396 
                   100459601 
                   0.728 
                   XPA 
                 
                 
                     
                   chr9 
                   100459482 
                   100459691 
                   0.724 
                   XPA 
                 
                 
                     
                   chr9 
                   100459482 
                   100459695 
                   0.720 
                   XPA 
                 
                 
                     
                   chr9 
                   100459482 
                   100459721 
                   0.721 
                   XPA 
                 
                 
                     
                   chrX 
                   14861796 
                   14861980 
                   0.416 
                   FANCB 
                 
                 
                     
                   chrX 
                   14861961 
                   14862165 
                   0.322 
                   FANCB 
                 
                 
                     
                   chrX 
                   14862588 
                   14862788 
                   0.368 
                   FANCB 
                 
                 
                     
                   chrX 
                   14862805 
                   14863005 
                   0.294 
                   FANCB 
                 
                 
                     
                   chrX 
                   14862977 
                   14863177 
                   0.358 
                   FANCB 
                 
                 
                     
                   chrX 
                   14863227 
                   14863447 
                   0.403 
                   FANCB 
                 
                 
                     
                   chrX 
                   14868691 
                   14868896 
                   0.306 
                   FANCB 
                 
                 
                     
                   chrX 
                   14871130 
                   14871330 
                   0.313 
                   FANCB 
                 
                 
                     
                   chrX 
                   14875743 
                   14875993 
                   0.307 
                   FANCB 
                 
                 
                     
                   chrX 
                   14877225 
                   14877425 
                   0.313 
                   FANCB 
                 
                 
                     
                   chrX 
                   14877435 
                   14877635 
                   0.274 
                   FANCB 
                 
                 
                     
                   chrX 
                   14882681 
                   14882881 
                   0.393 
                   FANCB 
                 
                 
                     
                   chrX 
                   14882885 
                   14883085 
                   0.328 
                   FANCB 
                 
                 
                     
                   chrX 
                   14883089 
                   14883289 
                   0.383 
                   FANCB 
                 
                 
                     
                   chrX 
                   14883275 
                   14883501 
                   0.291 
                   FANCB 
                 
                 
                     
                   chrX 
                   14883493 
                   14883735 
                   0.350 
                   FANCB 
                 
                 
                     
                   chrX 
                   14887070 
                   14887270 
                   0.323 
                   FANCB 
                 
                 
                     
                   chrX 
                   14890941 
                   14891170 
                   0.578 
                   FANCB 
                 
                 
                     
                   chrX 
                   47426013 
                   47426262 
                   0.636 
                   ARAF 
                 
                 
                     
                   chrX 
                   47426015 
                   47426263 
                   0.635 
                   ARAF 
                 
                 
                     
                   chrX 
                   47426016 
                   47426262 
                   0.640 
                   ARAF 
                 
                 
                     
                   chrX 
                   47426063 
                   47426266 
                   0.627 
                   ARAF 
                 
                 
                     
                   chrX 
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     DETAILED DESCRIPTION 
     The invention pertains to a method for analyzing tumor biomarker sequences that involves hybridization-based enrichment of selected target regions across the human genome in a multiplexed panel assay, followed by quantification, coupled with a novel bioinformatics and mathematical analysis pipeline. An overview of the method is shown schematically in  FIG. 1 . 
     In-solution hybridization enrichment has been used in the past to enrich specific regions of interest prior to sequencing (see e.g., Meyer, M and Kirchner, M. (2010)  Cold Spring Harb. Protoc.  2010(6):pdbprot5448; Liao, G. J. et al. (2012)  PLoS One  7:e38154; Maricic, T. et al. (2010)  PLoS One  5:e14004; Tewhey, R. et al. (2009)  Genome Biol.  10:R116; Tsangaras, K. et al. (2014)  PLoS One  9:e109101; PCT Publication WO 2016/189388; US Patent Publication 2016/0340733; Koumbaris, G. et al. (2016)  Clinical chemistry,  62(6), pp. 848-855). However, for the methods of the invention, the target sequences (referred to as TArget Capture Sequences, or TACS) used to enrich for specific regions of interest have been optimized for maximum efficiency, specificity and accuracy and, furthermore, in certain embodiments are used in families of TACS, comprising a plurality of members that bind to the same tumor biomarker sequence but with differing start and/or stop positions, such that enrichment of the tumor biomarker sequences of interest is significantly improved compared to use of a single TACS binding to the genomic sequence. An example of a configuration of such families of TACS is illustrated schematically in  FIG. 3 , showing that the different start and/or stop positions of the members of the TACS family when bound to the genomic sequence of interest results in a staggered binding pattern for the family members. 
     The use of families of TACS with the TACS pool that bind to each target sequence of interest, as compared to use of a single TACS within the TACS pool that binds to each target sequence of interest, significantly increases enrichment for the target sequences of interest, as evidenced by a greater than 50% average increase in read-depth for the family of TACS versus a single TACS. 
     Comparison of use of a family of TACS versus a single TACS, and the significantly improved read-depth that was observed, is described in detail in Example 5. 
     Tumor Biomarker Detection 
     The methods and kits of the disclosure are used in the analysis of tumor biomarkers in biological samples. As described in detail in Examples 6-9, the methods of the invention can used for the detection of large panels of tumor biomarkers at tumor loads as low as 0.1% and can detect tumor biomarkers in both tumor tissue and in liquid biopsy samples from tumor patients. Accordingly, in one aspect, the invention pertains to a method of detecting one or more tumor biomarkers in a DNA sample from a subject having or suspected of having a tumor, the method comprising: 
     (a) preparing a sequencing library from the DNA sample; 
     (b) hybridizing the sequencing library to a pool of double-stranded TArget Capture Sequences (TACS) that bind to one or more tumor biomarker sequences of interest, wherein:
         (i) each member sequence within the pool of TACS is between 100-500 base pairs in length, each member sequence having a 5′ end and a 3′ end;   (ii) preferably each member sequence binds to the tumor biomarker sequence of interest at least 50 base pairs away, on both the 5′ end and the 3′ end, from regions harboring Copy Number Variations (CNVs), Segmental duplications or repetitive DNA elements; and   (iii) the GC content of the pool of TACS is between 19% and 80%, as determined by calculating the GC content of each member within the pool of TACS;       

     (c) isolating members of the sequencing library that bind to the pool of TACS to obtain an enriched library; 
     (d) amplifying and sequencing the enriched library; and 
     (e) performing statistical analysis on the enriched library sequences, optionally utilizing only fragments of a specific size range, to thereby detect the tumor biomarker(s) in the DNA sample. 
     In one embodiment, the pool of TACS comprises a plurality of TACS families, wherein each member of a TACS family binds to the same tumor biomarker sequence of interest but with different start and/or stop positions on the sequence with respect to a reference coordinate system (i.e., binding of TACS family members to the target sequence is staggered) to thereby enrich for target sequences of interest, followed by massive parallel sequencing and statistical analysis of the enriched population. Typically, the reference coordinate system that is used for analyzing human genomic DNA is the human reference genome built hg19, which is publically available in the art, although other versions may be used. Alternatively, the reference coordinate system can be an artificially created genome based on built hg19 that contains only the genomic sequences of interest. Exemplary non-limiting examples of start/stop positions for TACS that bind to chromosome 13, 18, 21, X or Y are shown in  FIG. 2 . Exemplary non-limiting examples of start/stop positions for TACS that bind to NRAS on chromosome 1, PI3KCA on chromosome 3, EGFR on chromosome 7 or KRAS on chromosome 12 (as non-limiting examples of tumor biomarkers) are shown in  FIG. 10 . 
     Accordingly, in another aspect, the invention pertains to a method of detecting one or more tumor biomarkers in a DNA sample from a subject having or suspected of having a tumor, the method comprising: 
     (a) preparing a sequencing library from the DNA sample; 
     (b) hybridizing the sequencing library to a pool of double-stranded TArget Capture Sequences (TACS) that bind to one or more tumor biomarker sequences of interest, wherein the pool of TACS comprises a plurality of TACS families, wherein each member of a TACS family binds to the same tumor biomarker sequence of interest but with different start and/or stop positions on the sequence with respect to a reference coordinate system, and further wherein:
         (i) each member sequence within the pool of TACS is between 100-500 base pairs in length, each member sequence having a 5′ end and a 3′ end;   (ii) preferably each member sequence binds to the tumor biomarker sequence of interest at least 50 base pairs away, on both the 5′ end and the 3′ end, from regions harboring Copy Number Variations (CNVs), Segmental duplications or repetitive DNA elements; and   (iii) the GC content of the pool of TACS is between 19% and 80%, as determined by calculating the GC content of each member within the pool of TACS;       

     (c) isolating members of the sequencing library that bind to the pool of TACS to obtain an enriched library; 
     (d) amplifying and sequencing the enriched library; and 
     (e) performing statistical analysis on the enriched library sequences, optionally utilizing only fragments of a specific size range, to thereby detect the tumor biomarker(s) in the DNA sample. 
     The TACS-enrichment based method of the disclosure can be used in the detection of a wide variety of genetic abnormalities. In one embodiment, the genetic abnormality is a chromosomal aneuploidy (such as a trisomy, a partial trisomy or a monosomy). In other embodiments, the genomic abnormality is a structural abnormality, including but not limited to copy number changes including microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures. In another embodiment, the genetic abnormality is a chromosomal mosaicism. 
     Further aspects and features of the methods of the disclosure are described in the subsections below. 
     TArget Capture Sequence Design 
     As used herein, the term “TArget Capture Sequences” or “TACS” refers to short DNA sequences that are complementary to the region(s) of interest on a genomic sequence(s) of interest (e.g., chromosome(s) of interest) and which are used as “bait” to capture and enrich the region of interest from a large library of sequences, such as a whole genomic sequencing library prepared from a biological sample. In addition to the features of the families of TACS described above (e.g., staggered binding to the genomic sequence of interest), a pool of TACS is used for enrichment wherein the sequences within the pool have been optimized with regard to: (i) the length of the sequences; (ii) the distribution of the TACS across the region(s) of interest; and (iii) the GC content of the TACS. The number of sequences within the TACS pool (pool size) has also been optimized. 
     It has been discovered that TACS having a length of 100-500 base pairs are optimal to maximize enrichment efficiency. In various other embodiments, each sequence within the pool of TACS is between 150-260 base pairs, 100-200 base pairs, 200-260 base pairs, 100-350 bp in length, or 100-500 bp in length. In preferred embodiments, the length of the TACS within the pool is at least 250 base pairs, or is 250 base pairs or is 260 base pairs or is 280 base pairs. It will be appreciated by the ordinarily skilled artisan that a slight variation in TACS size typically can be used without altering the results (e.g., the addition or deletion of a few base pairs on either end of the TACS); accordingly, the base pair lengths given herein are to be considered “about” or “approximate”, allowing for some slight variation (e.g., 1-5%) in length. Thus, for example, a length of “250 base pairs” is intended to refer to “about 250 base pairs” or “approximately 250 base pairs”, such that, for example, 248 or 252 base pairs is also encompassed. 
     The distribution of the TACS across each region or chromosome of interest has been optimized to avoid, if applicable, high copy repeats, low copy repeats and copy number variants, while at the same time also being able to target informative single nucleotide polymorphisms (SN Ps) in order to enable both aneuploidy, or structural copy number change detection, and fraction of interest estimation. Accordingly, each sequence within the TACS pool is designed such that the 5′ end and the 3′ end are each at least 50 base pairs away from regions in the genome that are known to harbor one or more of the following genomic elements: Copy Number Variations (CNVs), Segmental duplications and/or repetitive DNA elements (such as transposable elements or tandem repeat areas). In various other embodiments, each sequence within the TACS pool is designed such that the 5′ end and the 3′ end are each at least 50, 100, 150, 200, 250, 300, 400 or 500 base pairs away from regions in the genome that are known to harbor one or more of the aforementioned elements. 
     The term “Copy Number Variations” is a term of art that refers to a form of structural variation in the human genome in which there can be alterations in the DNA of the genome in different individuals that can result in a fewer or greater than normal number of a section(s) of the genome in certain individuals. CNVs correspond to relatively large regions of the genome that may be deleted (e.g., a section that normally is A-B-C-D can be A-B-D) or may be duplicated (e.g., a section that normally is A-B-C-D can be A-B-C-C-D). CNVs account for roughly 13% of the human genome, with each variation ranging in size from about 1 kilobase to several megabases in size. 
     The term “Segmental duplications” (also known as “low-copy repeats”) is also a term of art that refers to blocks of DNA that range from about 1 to 400 kilobases in length that occur at more than one site within the genome and typically share a high level (greater than 90%) of sequence identity. Segmental duplications are reviewed in, for example, Eichler. E. E. (2001)  Trends Genet.  17:661-669. 
     The term “repetitive DNA elements” (also known as “repeat DNA” or “repeated DNA”) is also a term of art that refers to patterns of DNA that occur in multiple copies throughout the genome. The term “repetitive DNA element” encompasses terminal repeats, tandem repeats and interspersed repeats, including transposable elements. Repetitive DNA elements in NGS is discussed further in, for example, Todd, J. et al. (2012)  Nature Reviews Genet.  13:36-46. 
     The TACS are designed with specific GC content characteristics in order to minimize data GC bias and to allow a custom and innovative data analysis pipeline. It has been determined that TACS with a GC content of 19-80% achieve optimal enrichment and perform best with cell free DNA. Within the pool of TACS, different sequences can have different % GC content, although to be selected for inclusion with the pool, the % GC content of each sequence is chosen as between 19-80%, as determined by calculating the GC content of each member within each family of TACS. That is, every member within each family of TACS has a % GC content within the given percentage range (e.g., between 19-80% GC content). 
     In some instances, the pool of TACS (i.e., each member within each family of TACS) may be chosen so as to define a different % GC content range, deemed to be more suitable for the assessment of specific genetic abnormalities. Non-limiting examples of various % GC content ranges, can be between 19% and 80%, or between 19% and 79%, or between 19% and 78%, or between 19% and 77%, or between 19% and 76%, or between 19% and 75%, or between 19% and 74%, or between 19% and 73%, or between 19% and 72%, or between 19% and 71%, or between 19% and 70%, or between 19% and 69%, or between 19% and 68%, or between 19% and 67%, or between 19% and 66%, or between 19% and 65%, or between 19% and 64%, or between 19% and 63%, or between 19% and 62%, or between 19% and 61%, or between 19% and 60%, or between 19% and 59%, or between 19% and 58%, or between 19% and 57%, or between 19% and 56%, or between 19% and 55%, or between 19% and 54%, or between 19% and 53%, or between 19% and 52%, or between 19% and 51%, or between 19% and 50%, or between 19% and 49%, or between 19% and 48%, or between 19% and 47%, or between 19% and 46%, or between 19% and 45%, or between 19% and 44%, or between 19% and 43%, or between 19% and 42%, or between 19% and 41%, or between 19% and 40%. 
     As described in further detail below with respect to one embodiment of the data analysis, following amplification and sequencing of the enriched sequences, the test loci and reference loci can then be “matched” or grouped together according to their % GC content (e.g., test loci with a % GC content of 40% is matched with reference loci with a % GC content of 40%). It is appreciated that the % GC content matching procedure may allow slight variation in the allowed matched % GC range. A non-limiting instance, and with reference to the previously described example in text, a test locus with % GC content of 40% could be matched with reference loci of % GC ranging from 39-41%, thereby encompassing the test locus % GC within a suitable range. 
     To prepare a pool of TACS having the optimized criteria set forth above with respect to size, placement within the human genome and % GC content, both manual and computerized analysis methods known in the art can be applied to the analysis of the human reference genome. In one embodiment, a semi-automatic method is implemented where regions are firstly manually designed based on the human reference genome build 19 (hg19) ensuring that, if applicable, the aforementioned repetitive regions are avoided and subsequently are curated for GC-content using software that computes the % GC-content of each region based on its coordinates on the human reference genome build 19 (hg19). In another embodiment, custom-built software is used to analyses the human reference genome in order to identify suitable TACS regions that fulfill certain criteria, such as but not limited to, % GC content, proximity to repetitive regions and/or proximity to other TACS. 
     The number of TACS in the pool has been carefully examined and adjusted to achieve the best balance between result robustness and assay cost/throughput. The pool typically contains at least 800 or more TACS, but can include more, such as 1500 or more TACS, 2000 or more TACS or 2500 or more TACS or 3500 or more TACS or 5000 or more TACS. It has been found that an optimal number of TACS in the pool is 5000. It will be appreciated by the ordinarily skilled artisan that a slight variation in pool size typically can be used without altering the results (e.g., the addition or removal of a small number of TACS); accordingly, the number sizes of the pool given herein are to be considered “about” or “approximate”, allowing for some slight variation (e.g., 1-5%) in size. Thus, for example, a pool size of “1600 sequences” is intended to refer to “about 1600 sequences” or “approximately 1600 sequences”, such that, for example, 1590 or 1610 sequences is also encompassed. 
     In view of the foregoing, in another aspect, the invention provides a method for preparing a pool of TACS for use in the method of the invention for detecting risk of a chromosomal and/or other genetic abnormality, wherein the method for preparing the pool of TACS comprises: selecting regions in one or more chromosomes of interest having the criteria set forth above (e.g., at least 50 base pairs away on either end from the aforementioned repetitive sequences and a GC content of between 19% and 80%, as determined by calculating the GC content of each member within each family of TACS), preparing primers that amplify sequences that hybridize to the selected regions, and amplifying the sequences, wherein each sequence is 100-500 base pairs in length. 
     For use in the methods of the disclosure, the pool of TACS typically is fixed to a solid support, such as beads (such as magnetic beads) or a column. In one embodiment, the pool of TACS are labeled with biotin and are bound to magnetic beads coated with a biotin-binding substance, such as streptavidin or avidin, to thereby fix the pool of TACS to a solid support. Other suitable binding systems for fixing the pool of TACS to a solid support (such as beads or column) are known to the skilled artisan and readily available in the art. When magnetic beads are used as the solid support, sequences that bind to the TACS affixed to the beads can be separated magnetically from those sequences that do not bind to the TACS. 
     Families of TACS 
     In one embodiment, the pool of TACS comprises a plurality of TACS families directed to different tumor biomarker sequences of interest. Each TACS family comprises a plurality of members that bind to the same tumor biomarker sequence of interest but having different start and/or stop positions with respect to a reference coordinate system for the genomic sequence of interest. Typically, the reference coordinate system that is used for analyzing human genomic DNA is the human reference genome built hg19, which is publically available in the art, but other coordinate systems may also be used. Alternatively, the reference coordinate system can be an artificially created genome based on publically available coordinate systems, such as for example built hg19 of the human genome, that contains only the genomic sequences of interest. Exemplary non-limiting examples of start/stop positions for TACS that bind to chromosome 13, 18, 21, X or Y are shown in  FIG. 2 . 
     Each TACS family comprises at least 2 members that bind to the same genomic sequence of interest. In various embodiments, each TACS family comprises at least 2 member sequences, or at least 3 member sequences, or at least 4 member sequences, or at least 5 member sequences, or at least 6 member sequences, or at least 7 member sequences, or at least 8 member sequence, or at least 9 member sequences, or at least 10 member sequences. In various embodiments, each TACS family comprises 2 member sequences, or 3 member sequences, or 4 member sequences, or 5 member sequences, or 6 member sequences, or 7 member sequences, or 8 member sequences, or 9 member sequences, or 10 member sequences. In various embodiments, the plurality of TACS families comprises different families having different numbers of member sequences. For example, a pool of TACS can comprise one TACS family that comprises 3 member sequences, another TACS family that comprises 4 member sequences, and yet another TACS family that comprises 5 member sequences, and the like. In one embodiment, a TACS family comprises 3-5 member sequences. In another embodiment, the TACS family comprises 4 member sequences. 
     The pool of TACS comprises a plurality of TACS families. Thus, a pool of TACS comprises at least 2 TACS families. In various embodiments, a pool of TACS comprises at least 3 different TACS families, or at least 5 different TACS families, or at least 10 different TACS families, or at least 50 different TACS families, or at least 100 different TACS families, or at least 500 different TACS families, or at least 1000 different TACS families, or at least 2000 TACS families, or at least 4000 TACS families, or at least 5000 TACS families. 
     Each member within a family of TACS binds to the same genomic region of interest but with different start and/or stop positions, with respect to a reference coordinate system for the genomic sequence of interest, such that the binding pattern of the members of the TACS family is staggered (for example see  FIG. 3 ). In various embodiments, the start and/or stop positions are staggered by at least 3 base pairs, or at least 4 base pairs, or at least 5 base pairs, or at least 6 base pairs, or at least 7 base pairs, or at least 8 base pairs, or at least 9 base pairs, or at least 10 base pairs, or at least 15 base pairs, or at least 20 base pairs, or at least 25 base pairs. Typically, the start and/or stop positions are staggered by 5-10 base pairs. In one embodiment, the start and/or stop positions are staggered by 5 base pairs. In another embodiment, the start and/or stop positions are staggered by 10 base pairs. 
     Sample Collection and Preparation 
     The methods of the invention can be used with a variety of biological samples. Essentially any biological sample containing DNA, and in particular cell-free DNA (cfDNA), can be used as the sample in the methods, allowing for genetic analysis of the DNA therein. For example, a peripheral whole blood sample can be obtained from a subject and plasma can be obtained from the whole blood sample by standard methods. Total cell free DNA can then be extracted from the sample using standard techniques, non-limiting examples of which include a Qiasymphony protocol (Qiagen) suitable for cell free DNA isolation or any other manual or automated extraction method suitable for cell free DNA isolation. 
     For tumor biomarker detection, the sample is a biological sample obtained from a patient having or suspected of having a tumor. In one embodiment, the DNA sample comprises cell free tumor DNA (cftDNA). In one embodiment, the oncology sample is a sample of tissue (e.g., from a tumor biopsy). In another embodiment the sample is a patient&#39;s urine, sputum,ascites, cerebrospinal fluid or pleural effusion. In another embodiment, the oncology sample is a patient plasma sample, prepared from patient peripheral blood. Thus, the sample can be a liquid biopsy sample that is obtained non-invasively from a patient&#39;s blood sample, thereby potentially allowing for early detection of cancer prior to development of a detectable or palpable tumor, or can be from a tissue that has or is suspected of having cancer. In another embodiment, the oncology sample is a patient&#39;s healthy tissue such as buffy coat, prepared from patient peripheral blood, or buccal swab or healthy tissue adjacent to the tumor or another source of healthy cells. Thus, the healthy cells can provide a source of DNA that allows for detection of germline mutations and comparison with tumor DNA. 
     For the biological sample preparation, typically cells are lysed and DNA is extracted using standard techniques known in the art, a non-limiting example of which is the Qiagen DNeasy Blood and Tissue protocol. In another embodiment, cell free DNA is isolated from plasma using standard techniques, a non-limiting example of which is the Qiasymphony (Qiagen) protocol. 
     Following isolation, the cell free DNA of the sample is used for sequencing library construction to make the sample compatible with a downstream sequencing technology, such as Next Generation Sequencing. Typically this involves ligation of adapters onto the ends of the cell free DNA fragments, followed by amplification. Sequencing library preparation kits are commercially available. A non-limiting exemplary protocol for sequencing library preparation is described in detail in Example 1. In another embodiment, nuclear DNA (a non-limiting example of which is DNA extracted from tissue of buffy coat) is fragmented using standard techniques. A non-limiting example of DNA fragmentation is sonication. Fragmented nuclear DNA is then subjected to the same downstream procedures for cell free DNA described in this paragraph. 
     Enrichment by TACS Hybridization 
     The region(s) of interest on the chromosome(s) of interest (e.g., tumor biomarker sequences) is enriched by hybridizing the pool of TACS to the sequencing library, followed by isolation of those sequences within the sequencing library that bind to the TACS. To facilitate isolation of the desired, enriched sequences, typically the TACS sequences are modified in such a way that sequences that hybridize to the TACS can be separated from sequences that do not hybridize to the TACS. Typically, this is achieved by fixing the TACS to a solid support. This allows for physical separation of those sequences that bind the TACS from those sequences that do not bind the TACS. For example, each sequence within the pool of TACS can be labeled with biotin and the pool can then be bound to beads coated with a biotin-binding substance, such as streptavidin or avidin. In a preferred embodiment, the TACS are labeled with biotin and bound to streptavidin-coated magnetic beads. The ordinarily skilled artisan will appreciate, however, that other affinity binding systems are known in the art and can be used instead of biotin-streptavidin/avidin. For example, an antibody-based system can be used in which the TACS are labeled with an antigen and then bound to antibody-coated beads. Moreover, the TACS can incorporate on one end a sequence tag and can be bound to a solid support via a complementary sequence on the solid support that hybridizes to the sequence tag. Furthermore in addition to magnetic beads, other types of solid supports can be used, such as polymer beads and the like. 
     In certain embodiments, the members of the sequencing library that bind to the pool of TACS are fully complementary to the TACS. In other embodiments, the members of the sequencing library that bind to the pool of TACS are partially complementary to the TACS. For example, in certain circumstances it may be desirable to utilize and analyze data that are from DNA fragments that are products of the enrichment process but that do not necessarily belong to the genomic regions of interest (i.e. such DNA fragments could bind to the TACS because of part homologies (partial complementarity) with the TACS and when sequenced would produce very low coverage throughout the genome in non-TACS coordinates). 
     Following enrichment of the sequence(s) of interest using the TACS, thereby forming an enriched library, the members of the enriched library are eluted from the solid support and are amplified and sequenced using standard methods known in the art. Next Generation Sequencing is typically used, although other sequencing technologies can also be employed, which provides very accurate counting in addition to sequence information. To detect genetic abnormalities, such as but not limited to, aneuploidies or structural copy number changes requires very accurate counting and NGS is a type of technology that enables very accurate counting. Accordingly, for the detection of genetic abnormalities, such as but not limited to, aneuploidies or structural copy number changes, other accurate counting methods, such as digital PCR and microarrays can also be used instead of NGS. Non-limiting exemplary protocols for amplification and sequencing of the enriched library are described in detail in Example 3. 
     Data Analysis 
     The information obtained from the sequencing of the enriched library can be analyzed using an innovative biomathematical/biostatistical data analysis pipeline. Details of an exemplary analysis using this pipeline are described in depth in Example 4, and in further detail below. Alternative data analysis approaches for different purposes are also provided herein. For example, data analysis approaches for analyzing oncology samples are described in detail in Example 6-9 and in the oncology section below. 
     The analysis pipeline described in Example 4 exploits the characteristics of the TACS, and the high-efficiency of the target capture enables efficient detection of aneuploidies or structural copy number changes, as well as other types of genetic abnormalities. In the analysis, first the sample&#39;s sequenced DNA fragments are aligned to the human reference genome. QC metrics are used to inspect the aligned sample&#39;s properties and decide whether the sample is suitable to undergo classification. These QC metrics can include, but are not limited to, analysis of the enrichment patterns of the loci of interest, such as for example the overall sequencing depth of the sample, the on-target sequencing output of the sample, TACS performance, GC bias expectation, fraction of interest quantification. For determining the risk of a chromosomal abnormality in the DNA of the sample, an innovative algorithm is applied. The steps of the algorithm include, but are not limited to, removal of inadequately sequenced loci, read-depth and fragment-size information extraction at TACS-specific coordinates, genetic (GC-content) bias alleviation and ploidy status classification. 
     Ploidy status determination can be achieved using one or more statistical methods, non-limiting examples of which include a t-test method, a bootstrap method, a permutation test and/or a binomial test of proportions and/or segmentation-based methods and/or combinations thereof. It will be appreciated by the ordinarily skilled artisan that the selection and application of tests to be included in ploidy status determination is based on the number of data points available. As such, the suitability of each test is determined by various factors such as, but not limited to, the number of TACS utilized and the respective application for GC bias alleviation, if applicable. Thus, the aforementioned methods are to be taken as examples of the types of statistical analysis that may be employed and are not the only methods suitable for the determination of ploidy status. Typically, the statistical method results in a score value for the mixed sample and risk of the chromosomal abnormality in the DNA is detected when the score value for the mixed sample is above a reference threshold value. 
     In particular, one aspect of the statistical analysis involves quantifying and alleviating GC-content bias. In addition to the challenge of detecting small signal changes in DNA in the mixed sample, and/or other components of DNA of interest part of a mixed sample (for example, but not limited to, additional or less genetic material from certain chromosomal regions), the sequencing process itself introduces certain biases that can obscure signal detection. One such bias is the preferential sequencing/amplification of genetic regions based on their GC-content. As such, certain detection methods, such as but not limited to, read-depth based methods, need to account for such bias when examining sequencing data. Thus, the bias in the data needs to be quantified and, subsequently, suitable methods are applied to account for it such that genetic context dependencies cannot affect any statistical methods that may be used to quantify genetic abnormality risk. 
     For example, one method of quantifying the GC-content bias is to use a locally weighted scatterplot smoothing (LOESS) technique on the sequencing data. Each targeted locus may be defined by its sequencing read-depth output and its&#39; GC-content. A line of best fit through these two variables, for a large set of loci, provides an estimate of the expected sequencing read-depth given the GC-content. Once this GC-bias quantification step is completed, the next step is to use this information to account for possible biases in the data. One method is to normalize the read-depth of all loci by their expected read-depth (based on each locus&#39; GC-content). In principle, this unlinks the read-depth data from their genetic context and makes all data comparable. As such, data that are retrieved from different GC-content regions, such as for example, but not limited, to different chromosomes, can now be used in subsequent statistical tests for detection of any abnormalities. Thus, using the LOESS procedure, the GC bias is unlinked from the data prior to statistical testing. In one embodiment, the statistical analysis of the enriched library sequences comprises alleviating GC bias using a LOESS procedure. 
     In an alternative embodiment, the GC-content bias is quantified and alleviated by grouping together loci of similar (matching) GC-content. Thus, conceptually this method for alleviating GC-content bias comprises of three steps, as follows: 
     1) identification and calculation of GC-content in the TACS; 
     2) alleviation/accounting of GC-content bias using various matching/grouping procedures of the TACS; and 
     3) calculation of risk of any genetic abnormalities that may be present in the fetus utilizing statistical and mathematical methods on datasets produced from step 2. 
     For the t-test method, the dataset is split into two groups; the test loci and the reference loci. For each group, subsets of groups are created where loci are categorized according to their GC-content as illustrated in a non-limiting example in the sample Table 1 below: 
                                     TABLE 1                       GC   Reference loci read-depth   Test loci read-depth                          40%   x 1   40 , x 2   40 , . . . x nx40   40     y 1   40 , y 2   40 , . . . y ny40   40             41%   x 1   41 , x 2   41 , . . . x nx41   41     y 1   41 , y 2   41 , . . . y ny41   41             42%   x 1   42 , x 2   42 , . . . x nx42   42     y 1   42 , y 2   42 , . . . y ny42   42             . . .   . . .   . . .                        
It is appreciated by the ordinarily skilled artisan that subgroup creation may involve encompassing a range of appropriate GC-content and/or a subset of loci that are defined by a given GC-content and/or GC-content range. Accordingly, the % GC content given in the non-limiting example of Table 1 are to be considered “about” or “approximate”, allowing for some slight variation (e.g., 1-2%). Thus, for example, a % GC content of “40%” is intended to refer to “about 40%” or “approximately 40%”, such that, for example, “39%-41%” GC-content loci may also be encompassed if deemed appropriate.
 
     Hence, when referring to a particular GC-content it is understood that the reference and test loci subgroups may comprise of any number of loci related to a particular % GC content and/or range. 
     Subsequently, for each GC-content subgroup, a representative read-depth is calculated. A number of methods may be utilized to choose this such as, but not limited to, the mean, median or mode of each set. Thus, two vectors of representative read-depth are created where one corresponds to the reference loci and the other to the test loci (e.g., Xm, Ym). In one embodiment, the two vectors may be tested against each other to identify significant differences in read-depth. In another embodiment, the difference of the two vectors may be used to assess if there are significant discrepancies between the test and reference loci. The sample is attributed the score of the test. 
     For statistical analysis using a bootstrap approach, the dataset is split into two groups, the test loci and the reference loci. The GC-content of each locus is then calculated. Then the following procedure is performed: 
     A random locus is selected from the reference loci; its read-depth and GC-content are recorded. Subsequently, a random locus from the test loci is selected, with the only condition being that its&#39; GC-content is similar to that of the reference locus. Its read-depth is recorded. It is appreciated by the ordinarily skilled artisan that GC-content similarity may encompass a range of suitable GC-content. As such, referral to a specific % GC content may be considered as “approximate” or “proximal” or “within a suitable range” (e.g., 1%-2%) encompassing the specific % GC content under investigation. Thus, a reference-test locus pair of similar GC-content is created. The difference of the reference-test pair is recorded, say E1. The loci are then replaced to their respective groups. This process is repeated until a bootstrap sample of the same size as the number of test TACS present is created. A representative read-depth of the bootstrap sample is estimated, say E_mu, and recorded. A number of methods may be utilized to do so, such as but not limited to, the mean, mode or median value of the vector, and/or multiples thereof. 
     The process described above is repeated as many times as necessary and a distribution of E_mu is created. The sample is then attributed a score that corresponds to a percentile of this distribution. 
     For statistical analysis using a permutation test, the dataset is sorted firstly into two groups, the test-loci and the reference loci. For each group, subsets of groups are created, where loci are categorized according to their GC-content similarity (see columns 2 and 3 of the non-limiting sample Table 2 below). The number of loci present in each test subgroup is also recorded. The loci of the test group are utilized to calculate an estimate of the test-group&#39;s read-depth, say Yobs. A representative number from each GC-content subgroup may be selected to do so. Any number of methods may be used to provide a read-depth estimate, such as but not limited to, the mean, median or mode of the chosen loci. 
     
       
         
           
               
               
               
               
               
             
               
                 TABLE 2 
               
               
                   
               
               
                 GC 
                 Reference loci read-depth 
                 Test loci read-depth 
                 test loci 
                 Merging of loci 
               
               
                   
               
             
            
               
                 40% 
                 x 1   40 , x 2   40 , . . . x nx40   40   
                 y 1   40 , y 2   40 , . . . y ny40   40   
                 ny40 
                 x 1   40 , . . . x nx40   40 , y 1   40 , . . . y ny40   40   
               
               
                 41% 
                 x 1   41 , x 2   41 , . . . x nx41   41   
                 y 1   41 , y 2   41 , . . . y ny41   41   
                 ny41 
                 x 1   41 , . . . x nx41   41 , y 1   41 , . . . y ny41   41   
               
               
                 42% 
                 x 1   42 , x 2   42 , . . . x nx42   42   
                 y 1   42 , y 2   42 , . . . y ny42   42   
                 ny42 
                 x 1   42 , . . . x nx42   42 , y 1   42 , . . . y ny42   42   
               
               
                 . . . 
                 . . . 
                 . . . 
                 . . . 
                 . . . 
               
               
                   
               
            
           
         
       
     
     A distribution to test Yobs is then built utilizing loci irrespective of their test or reference status as follows. The test and reference loci of each GC-content subgroup (see last column of sample Table 2) are combined to allow for calculation of a new read-depth estimate. From each merged subgroup a number of loci are chosen at random, where this number is upper-bounded by the number of test-loci utilized in the original calculation of Yobs (e.g., for GC content 40%, and in the context of the non-limiting sample Table 2, this number of loci may be in the range [1,ny40]). The new read-depth estimate is calculated from all the chosen loci. The procedure is iterated as many times as necessary in order to build a distribution of observed means. A sample is then attributed a score that corresponds to the position of Yobs in this distribution using a suitable transformation that accounts for the moments of the built distribution. As with the already described methods, it is appreciated that slight variation in % GC content is allowed (e.g., 1%-2%), if deemed appropriate. Hence, reference to a specific GC-content could be taken as “about” or “approximate”, so that for example when referring to a 40% GC-content, loci that are “approximately” or “about” 40% (e.g., 39%-41%) may be utilized in the method. 
     For statistical analysis using a binomial test of proportions, fragment-sizes aligned to TACS-specific genomic coordinates are used. There is evidence from the literature that specific types of cancer can be characterized by and/or associated with fragments in the plasma having a smaller size than the expected size of fragments originating from healthy tissues (Jiang et al, (2015),  Proceedings of the National Academy of Sciences,  112(11), ppE1317-E1325). The same hypothesis holds true for fragments originating from the placenta/fetus. Specifically, it has been shown that fragments of cell free genetic material originating from the placenta tend to be smaller in length when compared to other cell free genetic material (Chan, K. C. (2004)  Clin. Chem.  50:88-92). Hence, the statistic of interest is whether the proportion of small-size fragments aligned to a TACS-specific test-region deviates significantly from what is expected when comparing it to the respective proportion of other TACS-specific reference-regions, as this would indicate fetal genetic abnormalities. 
     Thus, fragment-sizes are assigned into two groups. Sizes related to the test loci are assigned to one group and fragment-sizes related to the reference loci are assigned to the other group. Subsequently, in each group, fragment sizes are distributed into two subgroups, whereby small-size fragments are assigned into one subgroup and all remaining fragments are designated to the remaining subgroup. The last step computes the proportion of small-sized fragments in each group and uses these quantities in a binomial test of proportions. The score of the test is attributed to the sample under investigation. 
     The final result of a sample may be given by combining one or more scores derived from the different statistical methods, non-limiting examples of which are given in Example 4. 
     For statistical analysis using segmentation methods, the read-depth and sequence composition of non-overlapping genomic regions of interest of fixed-size is obtained. On the obtained dataset, GC-content read-depth bias alleviation may be performed, but is not limited to, using a local polynomial fitting method in order to estimate the expected read-depth of regions based on their GC content. The expected value, dependent on GC-content, is then used to normalize regions using suitable methods known to those skilled in the art. The normalized dataset is subsequently processed using one or more segmentation-based classification routines. To do so the algorithms process consecutive data points to detect the presence of read-depth deviations which manifest in the form of a “jump/drop” from their surrounding data points. Depending on the segmentation routine used, data points are given a score which is used towards assigning membership into segments of similar performing read-depths. For example, consecutive data points with score values within a suitable range may be classified as one segment, whereas consecutive data points with score values which exceed the set thresholds may be assigned to a different segment. 
     Kits of the Invention 
     In another aspect, the invention provides kits for carrying out the methods of the disclosure. In one embodiment, the kit comprises a container consisting of the pool of TACS and instructions for performing the method. In one embodiment, the TACS are provided in a form that allows them to be bound to a solid support, such as biotinylated TACS. In another embodiment, the TACS are provided together with a solid support, such as biotinylated TACS provided together with streptavidin-coated magnetic beads. 
     In one embodiment, the kit comprises a container comprising the pool of TACS and instructions for performing the method, wherein the pool of TACS comprises a plurality of TACS families, wherein each TACS family comprises a plurality of member sequences, wherein each member sequence binds to the same genomic sequence of interest (e.g., tumor biomarker sequence of interest) but has different start and/or stop positions with respect to a reference coordinate system for the genomic sequence of interest, and further wherein:
         (i) each member sequence within each TACS family is between 100-500 base pairs in length, each member sequence having a 5′ end and a 3′ end;   (ii) preferably each member sequence binds to the same genomic sequence of interest, and if applicable at least 50 base pairs away, on both the 5′ end and the 3′ end, from regions harboring Copy Number Variations (CNVs), Segmental duplications or repetitive DNA elements; and   (iii) the GC content of the pool of TACS is between 19% and 80%, as determined by calculating the GC content of each member within each family of TACS.       

     Furthermore, any of the various features described herein with respect to the design and structure of the TACS can be incorporated into the TACS that are included in the kit. 
     In various other embodiments, the kit can comprise additional components for carrying out other aspects of the method. For example, in addition to the pool of TACS, the kit can comprise one or more of the following (i) one or more components for isolating cell free DNA or nucleated DNA from a biological sample (e.g., as described in Example 1); 
     (ii) one or more components for preparing the sequencing library (e.g., primers, adapters, buffers, linkers, restriction enzymes, ligation enzymes, polymerase enzymes and the like as described in detail in Example 1); (iii) one or more components for amplifying and/or sequencing the enriched library (e.g., as described in Example 3); and/or (iv) software for performing statistical analysis (e.g., as described in Examples 4 and 6-11). 
     Oncology Uses 
     In various embodiments, the TACS-based enrichment method of the disclosure can be used for a variety of purposes in the oncology field. As described in detail in Examples 6-9, the method allows for detection of tumor biomarkers (including cancer related-germline mutations) in biological samples. The method can be applied to the analysis of essentially any known tumor biomarker. An extensive catalogue of known cancer-associated mutations is known in the art, referred to as COSMIC (Catalogue of Somatic Mutations in Cancer), described in, for example, Forbes, S. A. et al. (2016)  Curr. Protocol Hum. Genetic  91:10.11.1-10.11.37; Forbes, S. A. et al. (2017)  Nucl. Acids Res.  45:D777-D783; and Prior et al. (2012)  Cancer Res.  72:2457-2467. The COSMIC database is publically available at www.cancer.sanger.ac.uk. The database includes oncogenes that have been associated with cancers, any of which can be analyzed using the method of the disclosure. In addition to the COSMIC catalogue, other compilations of tumor biomarker mutations have been described in the art, non limiting examples of which include the ENCODE Project, which describes mutations in the regulatory sites of oncogenes (see e.g., Shar, N. A. et al. (2016)  Mol. Canc.  15:76) and ClinVar, a National Center for Biotechnology Information (NCBI) database for genomic variations associated with human health. The ClinVar database is publicly available at www.ncbi.nlm.nih.gov/clinvar. 
     The methods of the invention can be used to simultaneously analyze a large panel of tumor biomarkers in a single biological sample. For example, in various embodiments, the pool of TACS used in the method detects at least 5, or at least 10, or at least 15, or at least 20, or at least 25, or at least 30, or at least 35, or at least 40, or at least 45 or at least 50 different tumor biomarkers. 
     For detection of tumor biomarkers, TACS are designed based on the design criteria described herein and the known sequences of tumor biomarker genes and genetic mutations therein associated with cancer. In one embodiment, a plurality of TACS families used in the method bind to a plurality of tumor biomarker sequences of interest selected from the group comprising of ABL, AKT, AKT1, ALK, APC, AR, ARAF, ATM, BAP1, BARD1, BCL, BMPR1A, BRAF, BRCA, BRCA1, BRCA2, BRIP1, CDH1, CDKN, CHEK2, CTNNB1, DDB2, DDR2, DICER1, EGFR, EPCAM, ErbB, ErcC, ESR1, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FBXW7, FGFR, FLT, FLT3, FOXA1, FOXL2, GATA3, GNA11, GNAQ, GNAS, GREM1, HOX, HOXB13, HRAS, IDH1,JAK, JAK2, KEAP1, KIT, KRAS, MAP2Ks, MAP3Ks, MET, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, NBN, NPM1, NRAS, NTRK1, PALB2, PDGFRs, PI3KCs, PMS2, POLD1, POLE, POLH, PTEN, RAD50, RAD51C, RAD51D, RAF1, RB1, RET, RUNX1, SLX4, SMAD, SMAD4, SMARCA4, SPOP, STAT, STK11, TP53, VHL, XPA and XPC, and combinations thereof. 
     In one embodiment, the plurality of TACS families used in the method bind to a plurality of tumor biomarker sequences of interest selected from the group consisting of, but not limited to, EGFR_6240, KRAS_521, EGFR_6225, NRAS_578, NRAS_580, PIK3CA_763, EGFR_13553, EGFR_18430, BRAF_476, KIT_1314, NRAS_584, EGFR_12378, and combinations thereof. 
     Representative, exemplary and non-limiting examples of chromosomal start and stop positions for amplifying TACS that bind to exemplary, non-limiting tumor biomarker genes are shown in  FIG. 10 , for NRAS on chromosome 1, for PI3KCA on chromosome 3, for EGFR on chromosome 7 and for KRAS on chromosome 12. Alternative suitable chromosomal start and stop positions, for these oncogenes and/or for other oncogenes, for amplifying TACS are readily identifiable by one of ordinary skill in the art based on the teachings herein. 
     In one embodiment of the method, following sequencing of the library preparation and enrichment for the sequences of interest through TACS hybridization, the subsequent step of amplifying the enriched library is performed in the presence of blocking sequences that inhibit amplification of wild-type sequences. Thus, amplification is biased toward amplification of the mutant tumor biomarker sequences. 
     The pool of TACS and families of TACS used in the method of detecting tumor biomarkers can include any of the design features described herein with respect to the design of the TACS. For example, in various embodiments, each TACS family comprises at least 2, at least 3, at least 4 or at least 5 different member sequences. In one embodiment, each TACS family comprises 4 different member sequences. In various embodiments, the start and/or stop positions for the member sequences within a TACS family, with respect to a reference coordinate system for the genomic sequence of interest, are staggered by at least 5 base pairs, or at least 10 base pairs, or by 5-10 base pairs. In various embodiments, the pool of TACS comprises at least 5, or at least 10 or at least 50 or at least 100 different TACS families, or more. 
     Suitable statistical analysis approaches for use with oncology samples and detection of tumor biomarkers are described further in Examples 6-9. 
     The method for detecting tumor biomarkers can be used in a variety of different clinical circumstances in the oncology field. For example, the method can be used for making an initial cancer diagnosis in a subject suspected of having cancer. Accordingly in one embodiment, the method further comprises making a diagnosis of the subject based on detection of at least one tumor biomarker sequence. 
     Additionally, the method can be used to select an appropriate treatment regimen for a patient diagnosed with cancer, wherein the treatment regimen is designed to be effective against a tumor having the tumor biomarkers detected in the patient&#39;s tumor (i.e., known in the art as personalized medicine). Accordingly, in another embodiment, the method further comprises selecting a therapeutic regimen for the subject based on detection of at least one tumor biomarker sequence. 
     Still further, the method can be used to monitor the efficacy of a therapeutic regiment, wherein changes in tumor biomarker detection are used as an indicator of treatment efficacy. 
     Accordingly, in another embodiment, the method further comprises monitoring treatment efficacy of a therapeutic regimen in the subject based on detection of at least one tumor biomarker sequence. 
     Moreover, the method can be used to detect relapse and minimal residual disease (MRD), wherein detection of at least one tumor biomarker are used as an indicator of remaining tumor cells in a patient after treatment or tumor recurrence. Accordingly in another embodiment, the method further informs of MRD and disease relapse. 
     Also, the method can be used to detect cancer-related germline (hereditary) mutations in patients with cancer or individuals suspected of a cancer pre-disposing syndrome wherein detection of at least one germline mutation is used as an indicator for having a cancer pre-disposing syndrome. Accordingly, in another embodiment, the method further comprises diagnosing a patient or an individual with a hereditary cancer pre-disposing syndrome that can inform the clinician to allow for early medical intervention, treatment selection and close monitoring. 
     Fragment-Based Analysis 
     In another aspect, the invention pertains to fragment based analysis of samples, described further in Example 9. There is evidence from the literature that specific types of cancer can be characterized by and/or associated with fragments in the plasma having a smaller size than the expected size of fragments originating from healthy tissues (Jiang et al, (2015),  Proceedings of the National Academy of Sciences,  112(11), ppE1317-E1325). The same hypothesis holds true for fragments originating from the placenta/fetus. Specifically, placenta derived fragments are generally of smaller size when compared to fragments originating from maternal tissues/cells. Accordingly, a fragment size-based test was developed and assessed, demonstrating its ability to identify samples harboring chromosomal abnormalities. 
     Thus, the fragments-based detection may be used to detect abnormalities in mixed samples with low signal-to-noise ratio (e.g., as is the case in detection of cancer). 
     Accordingly, in one embodiment, a fragments-based test is utilized to detect the presence of somatic copy number aberrations in a sample from a patient suspected of having cancer. For example, a binomial test of proportions, as described Example 4 and Example 9, can be used for the detection of increased presence of nucleic acid material originating from non-healthy tissue (e.g., tumor tissue) based on fragment size. In particular, under the null hypothesis that the distribution of fragment sizes originating from both healthy and cancerous cells is the same, a binomial test for proportions (as described in Example 4 and Example 9) using continuity correction can be utilized to quantify any evidence against it. 
     EXAMPLES 
     The present invention is further illustrated by the following examples, which should not be construed as further limiting. The contents of all references, appendices, Genbank entries, patents and published patent applications cited throughout this application are expressly incorporated herein by reference in their entirety. 
     Example 1: Sample Collection and Library Preparation 
     The general methodology for the TACS-based multiplexed parallel analysis approach for genetic assessment is shown schematically in  FIG. 1 . In this example, methods for collecting and processing a maternal plasma sample (containing maternal and fetal DNA), followed by sequencing library preparation for use in the methodology of  FIG. 1  are described. The DNA sample and library preparation described herein can similarly be used with DNA samples from tumors for tumor biomarker detection (see Example 6-9). 
     Sample Collection 
     Plasma samples were obtained anonymously from pregnant women after the 10 th  week of gestation. Protocols used for collecting samples for our study were approved by the Cyprus National Bioethics Committee, and informed consent was obtained from all participants. 
     Sample Extraction 
     Cell Free DNA was extracted from 2-4 ml plasma from each individual using a manual or automated extraction method suitable for cell free DNA isolation such as for example, but not limited to, Qiasymphony protocol suitable for cell free fetal DNA isolation (Qiagen) (Koumbaris, G. et al. (2016) Clinical chemistry, 62(6), pp. 848-855). 
     Sequencing Library Preparation 
     Extracted DNA from maternal plasma samples was used for sequencing library construction. Standard library preparation methods were used with the following modifications. A negative control extraction library was prepared separately to monitor any contamination introduced during the experiment. During this step, 5′ and 3′ overhangs were filled-in, by adding 12 units of T4 polymerase (NEB) while 5′ phosphates were attached using 40 units of T4 polynucleotide kinase (NEB) in a 100 μl reaction and subsequent incubation at 25° C. for 15 minutes and then 12° C. for 15 minutes. Reaction products were purified using the MinElute kit (Qiagen). Subsequently, adaptors P5 and P7 (see adaptor preparation) were ligated at 1:10 dilution to both ends of the DNA using 5 units of T4 DNA ligase (NEB) in a 40 μl reaction for 20 minutes at room temperature, followed by purification using the MinElute kit (Qiagen). Nicks were removed in a fill-in reaction with 16 units of Bst polymerase (NEB) in a 40 μl reaction with subsequent incubation at 65° C. for 25 minutes and then 12° C. for 20 minutes. Products were purified using the MinElute kit (Qiagen). Library amplification was performed using a Fusion polymerase (Herculase II Fusion DNA polymerase (Agilent Technologies) or Pfusion High Fidelity Polymerase (NEB)) in 50 μl reactions and with the following cycling conditions, 95° C. for 3 minutes; followed by 10 cycles at 95° C. for 30 seconds, 60° C. for 30 seconds, 72° C. for 30 seconds and finally 72° C. for 3 minutes (Koumbaris, G. et al. (2016) Clinical chemistry, 62(6), pp. 848-855). The final library products were purified using the MinElute Purification Kit (Qiagen) and measured by spectrophotometry. 
     Adaptor Preparation 
     Hybridization mixtures for adapter P5 and P7 were prepared separately and incubated for 10 seconds at 95° C. followed by a ramp from 95° C. to 12° C. at a rate of 0.1° C./second. P5 and P7 reactions were combined to obtain a ready-to-use adapter mix (100 μM of each adapter). Hybridization mixtures were prepared as follows: P5 reaction mixture contained adaptor P5_F (500 μM) at a final concentration of 200 μM, adaptor P5+P7_R (500 μM) at a final concentration of 200 μM with 1× oligo hybridization buffer. In addition, P7 reaction mixture contained adaptor P7_F (500 μM) at a final concentration of 200 μM, adapter P5+P7_R (500 μM) at a final concentration of 200 μM with 1× oligo hybridization buffer (Koumbaris, G. et al. (2016)  Clinical chemistry,  62(6), pp.848-855.). Sequences were as follows, wherein *=a phosphorothioate bond (PTO) (Integrated DNA Technologies): 
     
       
         
           
               
               
            
               
                   
                 adaptor P5_F: 
               
               
                   
                 (SEQ ID NO: XX) 
               
               
                   
                 A*C*A*C*TCTTTCCCTACACGACGCTCTTCCG*A*T*C*T 
               
               
                   
                   
               
               
                   
                 adaptor P7_F: 
               
               
                   
                 (SEQ ID NO: YY) 
               
               
                   
                 G*T*G*A*CTGGAGTTCAGACGTGTGCTCTTCCG*A*T*C*T, 
               
               
                   
                   
               
               
                   
                 adaptor_P5+P7_R: 
               
               
                   
                 (SEQ ID NO: ZZ) 
               
               
                   
                 A*G*A*T*CGGAA*G*A*G*C. 
               
            
           
         
       
     
     Example 2: TArget Capture Sequences (TACS) Design and Preparation 
     This example describes preparation of custom TACS for the detection of whole or partial chromosomal abnormalities for chromosomes 13, 18, 21, X, Y or any other chromosome, as well as other genetic abnormalities, such as but not limited to, microdeletion/microduplication syndromes, translocations, inversions, insertions, and other point or small size mutations. The genomic target-loci used for TACS design were selected based on their GC content and their distance from repetitive elements (minimum 50 bp away). TACS size can be variable. In one embodiment of the method the TACS range from 100-500 bp in size and are generated through a PCR-based approach as described below. The TACS were prepared by simplex polymerase chain reaction using standard Taq polymerase, primers designed to amplify the target-loci, and normal DNA used as template. The chromosomal regions used to design primers to amplify suitable loci on chromosomes 13, 18, 21 and X, to thereby prepare the pool of TACS for analysis of chromosomes 13, 18, 21 and X, are shown in  FIG. 2 . 
     All custom TACS were generated using the following cycling conditions: 95° C. for 3 minutes; 40 cycles at 95° C. for 15 seconds, 60° C. for 15 seconds, 72° C. for 12 seconds; and 72° C. for 12 seconds, followed by verification via agarose gel electrophoresis and purification using standard PCR clean up kits such as the Qiaquick PCR Purification Kit (Qiagen) or the NucleoSpin 96 PCR clean-up (Mackerey Nagel) or the Agencourt AMPure XP for PCR Purification (Beckman Coulter). Concentration was measured by Nanodrop (Thermo Scientific). 
     Example 3: TACS Hybridization and Amplification 
     This example describes the steps schematically illustrated in  FIG. 1  of target capture by hybridization using TACS, followed by quantitation of captured sequences by Next Generation Sequencing (NGS). 
     TACS Biotinylation 
     TACS were prepared for hybridization, as previously described (Koumbaris, G. et al. (2016) Clinical chemistry, 62(6), pp. 848-855), starting with blunt ending with the Quick Blunting Kit (NEB) and incubation at room temperature for 30 minutes. Reaction products were subsequently purified using the MinElute kit (Qiagen) and were ligated with a biotin adaptor using the Quick Ligation Kit (NEB) in a 40 μlreaction at RT for 15 minutes. The reaction products were purified with the MinElute kit (Qiagen) and were denatured into single stranded DNA prior to immobilization on streptavidin coated magnetic beads (Invitrogen). 
     TACS Hybridization 
     Amplified libraries were mixed with blocking oligos (Koumbaris, G. et al. (2016) Clinical chemistry, 62(6), pp. 848-855) (200 μM), 5 μg of Cot-1 DNA (Invitrogen), 50 μg of Salmon Sperm DNA (Invitrogen), Agilent hybridization buffer 2×, Agilent blocking agent 10×, and were heated at 95° C. for 3 minutes to denature the DNA strands. Denaturation was followed by 30 minute incubation at 37° C. to block repetitive elements and adaptor sequences. The resulting mixture was then added to the biotinylated TACS. All samples were incubated in a rotating incubator for 12-48 hours at 66° C. After incubation, the beads were washed as described previously and DNA was eluted by heating (Koumbaris, G. et al. (2016)  Clinical chemistry,  62(6), pp. 848-855). Eluted products were amplified using outer-bound adaptor primers. Enriched amplified products were pooled equimolarly and sequenced on a suitable platform. 
     If appropriate, amplification may be biased toward amplification of specific/desired sequences. In one embodiment of the method, this is performed when amplification is performed in the presence of sequences that hybridize to the undesired sequence of interest, and as such block the action of the polymerase enzyme during the process. Hence, the action of the amplification enzyme is directed toward the sequence of interest during the process. 
     Example 4: Bioinformatics Sample Analysis 
     This example describes representative statistical analysis approaches for use in the methodology illustrated in  FIG. 1  (“analysis pipeline” in  FIG. 1 ). 
     Human Genome Alignment 
     For each sample, the bioinformatic pipeline routine described below was applied in order to align the sample&#39;s sequenced DNA fragments to the human reference genome. Targeted paired-end read fragments obtained from NGS results were processed to remove adaptor sequences and poor quality reads (Q-score&lt;25) using the cutadapt software (Martin, M. et al. (2011) EMB.netiournal 17.1). The quality of the raw and/or processed reads as well as any descriptive statistics which aid in the assessment of quality check of the sample&#39;s sequencing output were obtained using the FastQC software (Babraham Institute (2015) FastQC) and/or other custom-built software. Processed reads which were at least 25 bases long were aligned to the human reference genome built hg19 (UCSC Genome Bioinformatics) using the Burrows-Wheel Alignment algorithm (Li, H. and Durbin, R. (2009) Bioinformatics 25:1754-1760) but other algorithms known to those skilled in the art may be used as well. If relevant, duplicate reads were removed post-alignment. Where applicable, sequencing output pertaining to the same sample but processed on separate sequencing lanes, was merged to a single sequencing output file. The removal of duplicates and merging procedures were performed using the Picard tools software suite (Broad Institute (2015) Picard) and/or the Sambamba tools software suite (Tarasov, Artem, et al. “Sambamba: fast processing of NGS alignment formats.” Bioinformatics 31.12 (2015): 2032-2034.). A realignment procedure, using tools known to those in the art, may also be performed. 
     The above software analysis resulted in a final aligned version of a sequenced sample against the human reference genome and all subsequent steps were based on this aligned version. Information in terms of Short Nucleotide Polymorphisms (SNPs) at loci of interest was obtained using bcftools from the SAMtools software suite (Li, H. et al. (2009)  Bioinformatics  25:2078-2079) and/or other software known to those skilled in the art. The read-depth per base, at loci of interest, was obtained using the mpileup option of the SAMtools software suite, from here on referred to as the mpileup file. Information pertaining to the size of the aligned fragments was obtained using the view option of the SAMtools software suite, from here on referred to as the fragment-sizes file and/or other software known to those skilled in the art. 
     The mpileup file and the fragment-sizes file were processed using custom-build application programming interfaces (APIs) written in the Python and R programming languages (Python Software Foundation (2015)  Python ; The R Foundation (2015)  The R Project for Statistical Computing ). The APIs were used to determine the ploidy state of chromosomes of interest, and/or other genetic abnormalities in regions of interest across the human genome, using a series of steps (collectively henceforth referred to as the “algorithm”) and to also collect further descriptive statistics to be used as quality check metrics, such as but not limited to fetal fraction and/or fraction of interest quantification (collectively henceforth referred to as the “QC metrics”).The APIs can also be used for the assessment of genetic abnormalities from data generated when applying the described method in cases of multiple gestation pregnancies, as well as other genetic abnormalities such as, but not limited to, microdeletions, microduplications, copy number variations, translocations, inversions, insertions, point mutations and mutational signatures. 
     QC Metrics 
     QC metrics were used to inspect an aligned sample&#39;s properties and decide whether the sample was suitable to undergo classification. These metrics were, but are not limited to: 
     (a) The enrichment of a sample. The patterns of enrichment are indicative of whether a sample has had adequate enrichment across loci of interest in a particular sequencing experiment (herein referred to as a “run”). To assess this, various metrics are assessed, non-limiting examples of which are:
         (i) overall sample on-target read depth,   (ii) sample on-target sequencing output with respect to total mapped reads,   (iii) individual TACS performance in terms of achieved read-depth,   (iv) kurtosis and skewness of individual TACS enrichment,   (v) kurtosis and skewness moments that arise from all TACS,   (vi) fragment size distribution,   (vii) percentage of duplication,   (viii) percentage of paired reads and,   (ix) percentage of aligned reads,
 
if applicable.
 
The above checks are also taken into consideration with regards to GC-bias enrichment. Samples that fail to meet one or more of the criteria given above are flagged for further inspection, prior to classification.
       

     (b) A sample&#39;s fetal fraction or fraction of interest. Samples with an estimated fetal fraction, or fraction of interest, that is below a specific threshold are not classified. Furthermore, if applicable the fraction of interest may be calculated using more than one method and concordance of results between estimation methods may be used as an additional QC prior to classification. 
     The Algorithm 
     The algorithm is a collection of data processing, mathematical and statistical model routines arranged as a series of steps. The algorithm&#39;s steps aim in deciding the relative ploidy state of a chromosome of interest with respect to all other chromosomes of the sequenced sample and is used for the detection of whole or partial chromosomal abnormalities for chromosomes 13, 18, 21, X, Y or any other chromosome, as well as other genetic abnormalities such as, but not limited to, microdeletion/microduplication syndromes and other point or small size mutations. As such the algorithm can be used, but is not limited to, the detection of whole or partial chromosomal abnormalities for chromosomes 13, 18, 21, X,Y or any other chromosome, as well as other genetic abnormalities such as, but not limited to, microdeletions, microduplications, copy number variations, translocations, inversions, insertions, point mutations and other mutational signatures. The algorithm carries out, but is not limited to, two types of assessments, one pertaining to the read-depth information of each sample and the other to the distribution of fragment-sizes, across TACS-specific regions. One or more statistical tests may be associated with each type of assessment, non-limiting examples of which are given in the statistical methods described herein. 
     In the case of read-depth associated tests, the algorithm compares sequentially the read-depth of loci from each chromosome of interest (herein referred to as the test chromosome) against the read-depth of all other loci (herein referred to as the reference loci) to classify its ploidy state. For each sample, these steps were, but are not limited to: 
     (a) Removal of inadequately sequenced loci. The read-depth of each locus was retrieved. Loci that have not achieved a minimum number of reads, were considered as inadequately enriched and were removed prior to subsequent steps. 
     (b) Genetic (GC-content) bias alleviation. The sequencing procedure may introduce discrepancies in read-depth across the loci of interest depending on their GC content. To account for such bias, a novel sequence-matching approach that increases both sensitivity and specificity to detect chromosomal aneuploidies was employed. The GC content of each locus on the test chromosome was identified and similar genetic loci were grouped together to form genetically matched groups. The procedure was repeated for the reference loci. Then, genetically matched groups from the test chromosome were conditionally paired with their genetically matched group counterparts on the reference chromosome(s). The groups may have any number of members. The conditionally matched groups were then used to assess the ploidy status of test chromosomes. 
     (c) Genetic abnormality determination. Ploidy status determination, or other genetic abnormalities of interest such as but not limited to microdeletions, microduplications, copy number variations, translocations, inversions, insertions, point mutations and other mutational signatures was achieved using a single statistical method and/or a weighted score approach on the result from the following, but not limited to, statistical methods: 
     Statistical Method 1: The differences in read-depth of the conditionally paired groups were tested for statistical significance using the t-test formula: 
     
       
         
           
             t 
             = 
             
               
                 
                   x 
                   ^ 
                 
                 - 
                 μ 
               
               
                 s 
                 / 
                 
                   n 
                 
               
             
           
         
       
     
     where t is the result of the t-test, {circumflex over (x)} is the average of the differences of the conditionally paired groups, μ is the expected read-depth and is set to a value that represents insignificant read-depth differences between the two groups, s the standard deviation of the differences of the conditionally paired groups and n the length of the vector of the conditionally paired differences. The magnitude of the t-score was then used to identify evidence, if any, against the null hypothesis of same ploidy between reference and test chromosomes. Specifically, t&gt;=c1 (where c1 is a predefined threshold belonging to the set of all positive numbers) shows evidence against the null hypothesis of no difference. 
     Statistical Method 2: Bivariate nonparametric bootstrap. The bootstrap method depends on the relationship between the random variables X (read-depth of reference loci) and Y (read-depth of test loci). Here, the read depth of baits on the reference group (random variable denoted by X) were treated as the independent covariate. The first step of the iterative procedure involved random sampling with replacement (bootstrapping) of the read-depths of loci on the reference chromosomes, i.e. (x1,g1), . . . ,(xn,gn), where the parameter g is known and denotes the GC-content of the chosen bait. Then, for each randomly selected reference bait (xi,gi), a corresponding read depth was generated for a genetically matched locus i.e., (y1,g1), . . . ,(yn,gn). Thus, the bivariate data (x1,y1), (x2,y2), . . . ,(xn,yn) was arrived at, which was conditionally matched on their GC-content (parameter gi). The differences between the read depths of the genetically matched bootstrapped values xi and yi were used to compute the statistic of interest in each iteration. In one embodiment this statistical measure can be, but is not limited to, the mode, mean or median of the recorded differences, and/or multiples thereof. The procedure was repeated as necessary to build up the distribution of the statistic of interest from these differences. The sample was assigned a score that corresponds to a specific percentile of the built distribution (e.g. 5 th  percentile). Under the null hypothesis the ploidy between chromosomes in the reference and test groups is not different. As such, samples whose score for a particular chromosome, was greater than a predefined threshold, say c2, were classified as statistically unlikely to have the same ploidy. Other statistical measures may be employed. 
     Statistical Method 3: Stratified permutation test. The statistic of interest is the read-depth estimate of the test chromosome, denoted by    obs , which is calculated using all loci of the test chromosome&#39;s genetically matched groups as follows: 
     
       
         
           
             
               obs 
             
             = 
             
               
                 
                   ∑ 
                   
                     j 
                     = 
                     1 
                   
                   
                     j 
                     = 
                     T 
                   
                 
                 ⁢ 
                 
                   
                     ∑ 
                     
                       i 
                       = 
                       1 
                     
                     
                       i 
                       = 
                       Nj 
                     
                   
                   ⁢ 
                   
                     y 
                     ij 
                   
                 
               
               
                 
                   ∑ 
                   
                     j 
                     = 
                     1 
                   
                   
                     j 
                     = 
                     T 
                   
                 
                 ⁢ 
                 Nj 
               
             
           
         
       
     
     where y ij  is the read-depth of locus i part of the genetically matched group j (i.e., loci belonging to a specific group based on their GC-content), Nj is the number of test loci part of the genetically matched group j and T the number of genetically matched groups.
 
Subsequently, a null distribution to test    obs  was built. To do so, for each group j, the test and reference loci were combined (exchangeability under the null hypothesis), and each group j was sampled randomly up to Nj times without replacement (stratified permutation). This created a vector of values, say yi, and from this the vector&#39;s average value, say ý i ,was calculated. The procedure was repeated as necessary to build the null distribution. Finally    obs , was studentised against the null distribution using the formula:
 
     
       
         
           
             
               Z 
               Yobs 
             
             = 
             
               
                 
                   
                     Y 
                     obs 
                   
                   ^ 
                 
                 - 
                 
                   Y 
                   ^ 
                 
               
               
                 σ 
                 Y 
               
             
           
         
       
     
     where   and σ Y  are the first and square root of the second moment of all permuted statistic values. Samples whose Z yobs  was greater than a predefined threshold, say c3, were statistically less likely to have the same ploidy in the reference and test groups. 
     In the case of fragment-size associated tests, the algorithm computes the proportion of small-size fragments found in test-loci and compares it with the respective proportion in reference-loci as described in Statistical Method 4 below. 
     Statistical Method 4: Fragment Size Proportions. For each sample the number and size of fragments aligned onto the human reference genome at the corresponding TACS coordinates, is extracted. The data is subsequently filtered so as to remove fragment-sizes considered statistical outliers using the median outlier detection method. Specifically, outliers are defined as those fragments whose size is above or below the thresholds, F thr , set by equation: 
     where F median  is the median fragment-size of all fragments of a sample, X is a variable that can take values from the set of R+, and IQR is the interquartile range of fragment sizes. Thereafter, a binomial test of proportions is carried out to test for supporting evidence against the null hypothesis, H0, where this is defined as:
 
H0: The proportion of small fragments of the test-region is not different from the proportion of small-fragments of the reference region.
 
     In various embodiments of the invention, small fragments are defined as those fragments whose size is less than or equal to a subset of Z+, that is upper-bounded by 160 bp. If the set of all TACS are defined as T, then the test region can be any proper subset S which defines the region under investigation, and the reference region is the relative complement of S in T. For example, in one embodiment of the invention, the set S is defined by all TACS-captured sequences of chromosome 21 and thus the reference set is defined by all TACS-captured fragments on the reference chromosomes, and/or other reference loci 
     The alternative hypothesis, H1, is defined as: 
     H1: The proportion of small fragments of the test-region is not equal to the proportion of test fragments of the reference region. 
     As such, and taking into account continuity correction, the following score is computed (Brown et. al, Harrel): 
     
       
         
           
             
               W 
               test 
             
             = 
             
               
                 ( 
                 
                   
                     p 
                     ′ 
                   
                   - 
                   
                     p 
                     ref 
                   
                 
                 ) 
               
               / 
               
                 
                   
                     
                       p 
                       ′ 
                     
                     ⁡ 
                     
                       ( 
                       
                         1 
                         - 
                         
                           p 
                           ′ 
                         
                       
                       ) 
                     
                   
                   
                     N 
                     test 
                   
                 
               
             
           
         
       
       
         
           where 
         
       
       
         
           
             
               p 
               ′ 
             
             = 
             
               
                 ( 
                 
                   
                     F 
                     ′ 
                   
                   + 
                   0.5 
                 
                 ) 
               
               
                 ( 
                 
                   
                     N 
                     test 
                   
                   + 
                   1 
                 
                 ) 
               
             
           
         
       
       
         
           
             
               p 
               ref 
             
             = 
             
               
                 ( 
                 
                   
                     F 
                     ref 
                   
                   + 
                   0.5 
                 
                 ) 
               
               
                 ( 
                 
                   
                     N 
                     ref 
                   
                   + 
                   1 
                 
                 ) 
               
             
           
         
       
     
     {acute over (F)} is the number of small-size fragments on the test-region, F ref  the number of small size fragments on the reference region, N test the number of all fragments on the test region and N ref  the number of all fragments on the reference region. 
     For each sample, the algorithm tests sequentially the proportion of fragment sizes of regions under investigation (for example, but not limited to, chromosome 21, chromosome 18, chromosome 13 or other (sub)chromosomal regions of interest) against reference regions; those not under investigation at the time of testing. For each sample a score is assigned for each test. Scores above a set-threshold, say c4, provide evidence against the null hypothesis. 
     Weighted Score method 1: In one embodiment of the method, a weighted score was attributed to each samples, computed as a weighted sum of all statistical methods using the formula: 
         V   S ( R, F )= z   1 max{ R   S   , F   S }+(1− z   1 )min{ R   S   , F   S }
 
     where R S  is the run-specific corrected score arising from a weighted contribution of each read-depth related statistical method for sample s and is defined as: 
     
       
         
           
             
               R 
               s 
             
             = 
             
               
                 ( 
                 
                   
                     
                       Σ 
                       i 
                     
                     ⁢ 
                     
                       w 
                       i 
                     
                     ⁢ 
                     
                       S 
                       
                         i 
                         ⁢ 
                         s 
                       
                     
                   
                   - 
                   
                     
                       R 
                       ′ 
                     
                     r 
                   
                 
                 ) 
               
               
                 σ 
                 r 
               
             
           
         
       
     
     and Ŕ r is the run-specific median value calculated from the vector of all unadjusted read-depth related weighted scores that arise from a single sequencing run, and σ r  is a multiple of the standard deviation of R scores calculated from a reference set of 100 euploid samples. The terms max{R S , F S }and min{R S , F S } denote the maximum and minimum values of the bracketed set, respectively. F S  is the run-specific corrected score arising from the fragment-size related statistical method and is defined as: 
     
       
         
           
             
               F 
               s 
             
             = 
             
               
                 ( 
                 
                   
                     W 
                     test 
                   
                   - 
                   
                     
                       R 
                       ′ 
                     
                     f 
                   
                 
                 ) 
               
               
                 σ 
                 f 
               
             
           
         
       
     
     where W test  is as defined earlier, Ŕ f  is the run specific median calculated from the vector of all unadjusted fragment-related statistical scores that arise from a single sequencing run, and σ f  is a multiple of the standard deviation of F scores calculated from a reference set of 100 euploid samples. 
     A unique classification score of less than a predefined value indicates that there is no evidence from the observed data that a sample has a significant risk of aneuploidy. 
     Weighted Score method 2: In another embodiment of the method, the weighted score arising from the statistical methods described above was used to assign each sample a unique genetic abnormality risk score using the formula: 
     
       
         
           
             
               R 
               ⁡ 
               
                 ( 
                 
                   t 
                   , 
                   c 
                 
                 ) 
               
             
             = 
             
               
                 ∑ 
                 
                   j 
                   = 
                   0 
                 
                 
                   j 
                   = 
                   N 
                 
               
               ⁢ 
               
                 
                   w 
                   j 
                 
                 ⁢ 
                 
                   
                     t 
                     j 
                   
                   
                     c 
                     j 
                   
                 
               
             
           
         
       
     
     where R is the weighted score result, w j  the weight assigned to method j, t j  the observed score resulting from method j, and c j  the threshold of method j. 
     A unique classification score of less than a predefined value indicates that there is no evidence from the observed data that a sample has a significant risk of aneuploidy. 
     Since all read depths from baits in the reference group were assumed to be generated from the same population, and in order to have a universal threshold, run-specific adjustments were also employed to alleviate run-specific biases. 
     The aforementioned method(s), are also suitable for the detection of other genetic abnormalities, such as but not limited to, subchromosomal abnormalities. A non-limiting example is the contiguous partial loss of chromosomal material leading to a state of microdeletion, or the contiguous partial gain of chromosomal material leading to a state of microduplication. A known genetic locus subject to both such abnormalities is 7q11.23. In one embodiment of statistical method 1, synthetic plasma samples of 5%, 10% and 20% fetal material were tested for increased risk of microdeletion and/or microduplication states for the genetic locus 7q11.23. 
     For point mutations various binomial tests are carried out that take into consideration the fetal fraction estimate of the sample, f, the read-depth of the minor allele, r, and the total read-depth of the sequenced base, n. Two frequent, yet non-limiting examples involve assessment of the risk when the genetic abnormality is a recessive point mutation or a dominant point mutation. 
     In the non-limiting example of a recessive point mutation the null hypothesis tested is that both the mother and the fetus are heterozygous (minor allele frequency is 0.5) against the alternative in which the fetus is homozygous (minor allele frequency is 0.5-f/2). A small p-value from the corresponding likelihood ratio test would indicate evidence against the null. In the non-limiting example of a dominant point mutation the null hypothesis tested is that the mother and fetus are homozygous at the given position against the alternative in which only the fetus is heterozygous for the given position. A small p-value from the corresponding likelihood ratio test would indicate evidence against the null. 
     In addition to the above, fetal sex determination methods were also developed, with non-limiting examples given below. In one embodiment of the invention, fetal sex was assigned to a sample using a Poisson test using the formula: 
     
       
         
           
             
               Pr 
               ⁡ 
               
                 ( 
                 
                   
                     r 
                     y 
                   
                   ≤ 
                   k 
                 
                 ) 
               
             
             = 
             
               
                 e 
                 
                   - 
                   λ 
                 
               
               ⁢ 
               
                 
                   ∑ 
                   
                     i 
                     = 
                     0 
                   
                   
                     i 
                     = 
                     k 
                   
                 
                 ⁢ 
                 
                   
                     λ 
                     i 
                   
                   
                     i 
                     ! 
                   
                 
               
             
           
         
       
       
         
           where 
         
       
       
         
           
             λ 
             = 
             
               
                 fE 
                 ⁢ 
                 
                     
                 
                 ⁢ 
                 μ 
               
               2 
             
           
         
       
     
     and f is the fetal fraction estimate of the sample, B is the number of target sequences on chromosome Y, μ is the read-depth of the sample and k is the sum of reads obtained from all targets B. The null hypothesis of the Poisson test was that the sample is male. A value of Pr(r y ) less than a threshold c y  was considered as enough evidence to reject the null hypothesis, i.e. the sample is not male. If any of the terms for computing Pr(r y ) were unavailable, then the sample&#39;s sex was classified as NA (not available). 
     In another embodiment of the invention, fetal sex was assigned using the average read-depth of target sequences on chromosome Y. If the average read-depth of the target-sequences was over a predefined threshold, where such threshold may be defined using other sample-specific characteristics such as read-depth and fetal-fraction estimate, the fetal sex was classified as male. If the average read-depth was below such threshold then the sample was classified as female. 
     Fetal Fraction Estimation/Fraction of Interest Estimation 
     Several methods have been developed to estimate fetal fraction that can be applied to singleton and/or to multiple gestation pregnancies. As such, and dependent on the type of pregnancy, the fetal fraction estimate can be obtained from either method or as a weighted estimate from a subset and/or all developed methods. Some non-limiting examples are given below. 
     In one embodiment, a machine learning technique has been developed based on Bayesian inference to compute the posterior distribution of fetal DNA fraction using allelic counts at heterozygous loci in maternal plasma of singleton pregnancies. Three possible informative combinations of maternal/fetal genotypes were utilized within the model to identify those fetal DNA fraction values that get most of the support from the observed data. 
     Let f denote the fetal DNA fraction. If the mother is heterozygous at a given genomic locus, the fetal genotype can be either heterozygous or homozygous resulting in expected minor allele frequencies at 0.5 and 0.5-f/2, respectively. If the mother is homozygous and the fetus is heterozygous then the expected minor allele frequency will be f/2. A Markov chain Monte Carlo method (a Metropolis-Hastings algorithm) (The R Foundation (2015)  The R Project for Statistical Computing ) was used with either a non-informative or an informative prior (i.e. incorporate additional information such as gestational age, maternal weight etc.) to obtain a sequence of random samples from the posterior probability distribution of fetal DNA fraction that is based on a finite mixture model. 
     In another embodiment, the fetal fraction estimate is computed only from the fetus-specific minor allele frequency (MAF) cluster, i.e. the cluster formed when the mother is homozygous and the fetus is heterozygous for a given genomic locus. It is assumed that the mean value of the fetal fraction estimate is normally distributed as N(2{acute over (x)}, σ {acute over (x)} ), where {acute over (x)} is the mean of the fetus-specific MAF, and σ {acute over (x)}  is the standard deviation of the fetus-specific MAF. The fetal fraction estimate is then obtained from percentiles of the computed distribution, N(2{acute over (x)}, σ {acute over (x)}).    
     For multiple gestation pregnancies, non-limiting examples of which include monozygotic and dizygotic twin pregnancies, triplet pregnancies and various egg and/or sperm donor cases, the fetal fraction can he estimated using information obtained from heterozygous genetic loci whose MAF value is less than a threshold, say M thresh , and derived from potential fetus-specific SNPs. The ordinarily skilled artisan will appreciate that fetus specific SNPs can originate from any fetus, or from any possible combination of the fetuses or from all the fetuses of the gestation. As such, an algorithm that estimates the fetal fraction of the fetus with the smallest contribution to the total fetal content, by taking into account the combinatorial contribution of each fetus to the MAF values that define fetus-specific SNPs, and also allows for inhomogeneous contribution of fetal material to the total fetal content of plasma derived material has been developed. To this effect, a two-step approach is employed by the algorithm. 
     In one embodiment of the algorithm, the multiple gestation pregnancy under consideration is a dizygotic twin pregnancy. As a first step, the algorithmic implementation of the model utilizes all informative SNPs and allows for inhomogeneous fetal contribution that can be explained with a fold-difference in fetal fraction estimates of a set threshold, say cf. Specifically, if f1 and f2 represent the fetal fractions of fetus one and fetus two, and f1&lt;=f2, then the assumption is that f2&lt;=cf f1, with cf being a positive real number greater than or equal to 1. Under this assumption, the observed data D, defined as counts of the alternate and reference alleles at informative SNP loci, are believed to be generated from a mixture distribution of three Binomials (defined by parameters, f1/2, f2/2 and (f1+f2)/2), with the posterior distribution p(f1,f2|D) being proportional to the observational model which can be written as p(f1|f2,D) p(f2|D). The posterior distribution p(f1,f2|D) is sampled with an MCMC Metropolis-Hastings algorithm using a uniform prior. The empirical quantile approach is performed on the generated data array to infer the fetal fractions. 
     As a second step, the algorithm runs a model-based clustering algorithm (Finite Gaussian mixture modeling fitted via EM algorithm; R-package: mclust) to identify whether there exists a separate outlier SNP cluster which is believed to be centered around f1/2. Existence of such a cluster with a mean invalidating the cf&gt;=f2/f1 assumption, leads to estimation of f1 using only SNPs part of the identified cluster. 
     The methods described above are suited to the determination of the fraction of any component of interest part of a mixed sample. As such, the methods are not to be understood as applicable only to the application of fetal fraction estimation and can be applied to the estimation of any component of interest part of a mixed sample, as outlined in Example 6. 
     Example 5: Target Enrichment Using Families of TACS 
     In this example, a family of TACS, containing a plurality of members that all bind to the same target sequence of interest, was used for enrichment, compared to use of a single TACS binding to a target sequence of interest. Each member of the family of TACS bound to the same target sequence of interest but had different start/stop coordinates with respect to a reference coordinate system for that target sequence (e.g., the human reference genome, built hg19). Thus, when aligned to the target sequence, the family of TACS exhibit a staggered binding pattern, as illustrated in  FIG. 3 . Typically, the members of a TACS family were staggered approximately 5-10 base pairs. 
     A family of TACS containing four members (i.e., four sequences that bound to the same target sequence but having different start and/or stop positions such that the binding of the members to the target sequence was staggered) was prepared. Single TACS hybridization was also prepared as a control. The TACS were fixed to a solid support by labelling with biotin and binding to magnetic beads coated with a biotin-binding substance (e.g., streptavidin or avidin) as described in Example 3. The family of TACS and single TACS were then hybridized to a sequence library, bound sequences were eluted and amplified, and these enriched amplified products were then pooled equimolarly and sequenced on a suitable sequencing platform, as described in Example 3. 
     The enriched sequences from the family of TACS sample and the single TACS sample were analyzed for read-depth. The results are shown in  FIGS. 4A and 4B . As shown in  FIG. 4A , target sequences of interest enriched using the family of four TACS (red dots) exhibited a fold-change in read-depth when compared to control sequences that were subjected to enrichment using only a single TACS (blue dots). Fold-change was assessed by normalizing the read-depth of each locus by the average read-depth of a sample, wherein the average read-depth was calculated from all loci enriched with a single TACS. As shown in  FIG. 4B , an overall 54.7% average increase in read-depth was observed using the family of four TACS. 
     This example demonstrates that use of a family of TACS, as compared to a single TACS, results in significantly improved enrichment of a target sequence of interest resulting in significantly improved read-depth of that sequence. 
     Example 6: Tumor Biomarker Detection in Reference Material 
     In this example, the TACS methodology, illustrated in  FIG. 1 , was used for the detection of tumor biomarkers in certified reference material known to harbor particular genetic mutations that are tumor biomarkers. For detection of the tumor biomarker sequences of interest, families of TACS, as described in Example 5, were used. 
     A sample of certified reference material harboring known tumor-associated genetic mutations was commercially obtained and samples were prepared to simulate tumor loads of 0.1%, 1.0% and 5.0%. 
     The samples were subjected to the TACS methodology illustrated in  FIG. 1  using families of TACS that bound to the following tumor-associated genetic mutations: EGFR_6240, KRAS_521, EGFR_6225, NRAS_578, NRAS_580, PIK3CA_763, EGFR_13553, EGFR_18430. 
     Following amplification and sequence of the TACS-enriched products, data analysis was performed as follows. Sequencing products were processed to remove adaptor sequences and poor quality reads. Reads whose length was at least 25 bases long post adaptor-removal were aligned to either: 
     (a) the human reference genome built hg19, or 
     (b) an artificially created genome based on built hg19 which contains only sequences of interest. 
     If relevant, duplicate reads were removed post-alignment. Where applicable, sequencing output pertaining to the same sample but processed on separate sequencing lanes was merged to a single sequencing output file. Local realignment of the data, using tools known in the art, may also be performed. The above software analysis provided a final aligned version of a sequenced sample against the reference genome, defined here as the final BAM file, where information can be extracted from it in terms of Short Nucleotide Polymorphisms (SNPs), Single Nucleotide Variants (SNVs) and other genetic variations with respect to a reference sequence at loci of interest, read-depth per base and the size of aligned fragments. Various available tools known to those skilled in the art, such as but not limited to bcftools, which is part of the samtools software suite, or varDict can be used to collect SNP information from the final BAM file. Such information concerns the sequence and number of times each variant is present in a sequenced sample was detected and was used to 
     (a) infer the presence of a genetic mutation, and 
     (b) to estimate the tumor load using the fetal-fraction estimation/fraction of interest estimation method described in Example 4. 
     In addition to the detection of the genetic mutation, statistical confidence was ascribed to a detected mutation using the estimated tumor load of the sample and the read-depth of each of the detected variants at a given position using binomial statistics. More than one test may be employed from which one can compute the probability of obtaining the sequenced information, or obtain a 95% confidence interval which describes a range of possible read-depths for the genetic mutation, or whether the obtained proportion of reads which can be ascribed to the genetic mutation is consistent with what would be expected at the given tumor load. A suitable binomial test of proportions is described in Example 4 (in the context of classification of chromosomal abnormalities). 
     The results are shown in  FIG. 5 . The line illustrates the expected minor allele frequency (MAF) for each percent (%) tumor load. The bars (x-axis) illustrate the detected MAF (y-axis) for each sample for the indicated genetic mutations. Two technical replicates are shown for the reference material. 
     The data demonstrates that the TACS methodology successfully detected the tumor-associated genetic mutations EGFR_6240, KRAS_521, EGFR_6225, NRAS_578, NRAS_580, PIK3CA_763, EGFR_13553 and EGFR_18430 at the expected tumor loads of 1.0% and 5.0%. Mutations EGFR_6240, NRAS_578, PIK3CA_763, EGFR_13553 and EFGR_18430 were also successfully detected at 0.1% tumor load. 
     Accordingly, this example demonstrates the successful detection of a large panel of different tumor biomarkers using the TACS methodology at tumor loads as low as 0.1%. 
     Example 7: Tumor Biomarker Detection in Patient Samples 
     In this example, the TACS methodology, illustrated in  FIG. 1 , was used for the detection of tumor biomarkers in tumor tissue and blood plasma samples from untreated cancer patients with confirmed diagnosis. For detection of the tumor biomarker sequences of interest, families of TACS, as described in Example 5, were used. 
     Matched pairs of peripheral blood and tumor tissue samples from untreated cancer patients were used to further validate the performance of the TACS methodology for tumor biomarker detection for a patient harboring mutation PIK3CA E545K (Patient 1) and for a patient harboring mutation TP53 K139 (Patient 2). The results are shown in  FIG. 6 . 
     As shown in  FIG. 6 , application of the TACS methodology to a tissue sample obtained from Patient 1 harboring mutation PIK3CA E545K (top bars) provided a variant allele frequency (VAF) percentage (i.e., the percentage that the genetic mutation is present instead of the normal allele) of ˜62%. Plasma obtained from peripheral blood of Patient 1 was processed according to the method described in Example 1 and provided a 6.05% VAF. Similarly, application of the TACS methodology to samples obtained from Patient 2 harboring mutation TP53 K139 (bottom bars) provided a VAF of ˜60% for tumor tissue and a VAF of 4.88% for plasma obtained from a peripheral blood sample. 
     Accordingly, this example demonstrates the successful detection of tumor biomarkers in cancer patient samples, in both tumor tissue samples and plasma samples, thereby demonstrating the suitability of the TACS methodology for tissue biopsy and for non-invasive tumor biomarker detection using liquid biopsy. 
     Example 8: Detection of Mutational Profiles 
     Given the ability of the TACS methodology illustrated in  FIG. 1  to detect a number of somatic single nucleotide variations (SNVs), these can be examined in the context of motifs, also referred to as mutational profiles. Most somatic mutations in tumors can be considered as passengers and may not be associated with pathogenesis if examined individually. Nonetheless, examining the profile of detected mutations as a whole can be useful in determining and/or detecting a pathogenesis-associated mutational profile. Various algorithms have been developed to decompose known mutational motifs operative in many cancer types. Alternatively, other metrics utilizing specific characteristics such as the type of mutations detected in the context of their neighboring bases can be utilized to this effect. The developed algorithms can infer the most likely scenario(s) that explain the observed data. Decomposition of the number and types of known mutational patterns/signatures that have, most likely, generated the observed mutational profile has been achieved using, but not limited to, the Lawson-Hanson non-negative least squares algorithm. 
       FIG. 7  shows the observed pattern of somatic SNVs for breast cancer using data downloaded from the COSMIC database. The x-axis shows a single base mutation observed in cancer in the context of its neighboring sequences. For example A[C&gt;A]T describes the mutation of Cytosine (C) to Adenine (A) where the upstream sequence is Adenine and the downstream sequence is Thymine. The y-axis shows the frequency of occurrence of this mutation in breast cancer. 
       FIG. 8  illustrates the results of a simulations study where mutational profiles were randomly generated by sampling a subset of SNVs each time, from data available in the COSMIC database, thereby simulating individuals. The simulated data were then subjected to the decomposition algorithms described above in order to detect the likely underlying mutational motifs. The bars indicate the average estimated frequency of the known mutational breast signatures computed from a data set of 10000 simulations. The developed algorithm shows evidence of detection of the mutational profiles, thereby demonstrating that detection of mutational profiles, or motifs, is possible using the developed algorithms. 
     Example 9: Fragment Size Based Tests 
     There is evidence from the literature that specific types of cancer can be characterized by and/or associated with fragments in the plasma having a smaller size than the expected size of fragments originating from healthy tissues (Jiang et al, (2015),  Proceedings of the National Academy of Sciences,  112(11), ppE1317-E1325). Thus, a fragments-size based test can be utilized to detect the presence of somatic copy number variations in individuals suspected of having cancer. To this effect, a binomial test of proportions, as described Example 4, can be used for the detection of increased presence of nucleic acid material originating from non-healthy tissue (e.g., tumor tissue) based on fragment size. In particular, under the null hypothesis that the distribution of fragment sizes originating from both healthy and non-healthy cells (for example, but not limited to cancerous cells) is the same, a binomial test for proportions (as described in Example 4) using continuity correction can be utilized to quantify any evidence against it. 
     The same hypothesis holds true for fragments originating from the placenta/fetus. Specifically, placenta derived fragments are generally of smaller size when compared to fragments originating from maternal tissues/cells. Accordingly, assessment of the fragment size-based test was performed using maternal plasma samples (i.e., mixed samples where cell free DNA is of maternal and fetal origin). The size of fragments that have aligned to TACS-enriched regions can be obtained from the aligned data. Subsequently, the proportion of fragments under a specific threshold from a test region is compared respective proportion of fragments from a reference region for evidence against the null hypothesis H0, 
     H0: The proportion of small fragments of the test-region is not different from the proportion of small-fragments of the reference region. 
       FIG. 9  shows results when applying the fragment sizes method to the mixed sample containing maternal and fetal DNA. The black dots are individual samples. The x-axis shows the sample index. The y-axis shows the score result of the fragments-based method. A score result greater than the one indicated by the threshold, illustrated as a grey line, indicates a deviation from the expected size of fragments illustrating the presence of aneuploidy. The results demonstrate that an aneuploid sample, having an estimated fetal fraction equal to 2.8%, was correctly identified, illustrating that fragments-based detection may be used to detect abnormalities in mixed samples with low signal-to-noise ratio (e.g., as is the case in detection of cancer). 
     Accordingly, this example demonstrates the successful ability of the fragments-based detection method in detecting genetic abnormalities in mixed samples with low signal-to-noise ratios, thereby demonstrating the suitability of the fragments-based test for analysis of either cancer samples for oncology purposes or maternal samples for NIPT. 
     Since small-sized fragments are associated with fragments from non-healthy tissues (Jiang et al, (2015),  Proceedings of the National Academy of Sciences,  112(11), ppE1317-E1325) they can also be leveraged for the detection of small-sized mutations, such as point mutations and mutational signatures. For example, one may only use small-sized fragments in Variant Allele Frequency estimation as described in examples 6-9, thereby increasing the signal-to-noise ratio. 
     Example 10: Use of the Method for Tissue Biopsies 
     Five FFPE samples from Breast carcinoma and 13 tissue samples (fresh/frozen and FFPE) from lung adenocarcinoma were subjected to the method and the mutational status was successfully detected. The data are presented below. 
     Breast Carcinoma 
       
     
       
         
           
               
               
               
               
               
               
               
             
               
                   
               
               
                 Type of 
                   
                   
                   
                   
                   
                   
               
               
                 specimen 
                 Patient ID 
                 Gene 
                 CDS mutation 
                 AA change 
                 COMSIC ID 
                 MAF % 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 FFPE 
                 BCa1 
                 TP53 
                 c.569delC 
                 p.190fs*57 
                 COSM100030 
                 17.39 
               
               
                   
                   
                 TP53 
                 c.559 + 25G &gt; A 
                 intronic 
                 COSM45841 
                 22.22 
               
               
                 FFPE 
                 BCa2 
                 PIK3CA 
                 c.1624G &gt; A 
                 P.E542K 
                 COSM760 
                 32.15 
               
               
                   
                   
                 FLT3 
                 c.2501G &gt; A 
                 P.R834Q 
                 COSM28047 
                 2.01 
               
               
                 FFPE 
                 BCa3 
                 ALK 
                 C.3515 + 18C &gt; T 
                 intronic 
                 COSM28496 
                 49.43 
               
               
                 FFPE 
                 BCa4 
                 AKT1 
                 c.49G &gt; A 
                 p.E17K 
                 COSM33765 
                 42.86 
               
               
                 FFPE 
                 BCa5 
                 PIK3CA 
                 c.1633G &gt; A 
                 E545K 
                 COSM763 
                 62.79 
               
               
                   
                   
                 PTEN 
                 C.1-9C &gt; G 
                 intronic 
                 COSM5915 
                 26.19 
               
               
                   
                   
                 TP53 
                 c.415A &gt; T 
                 p.K139* 
                 COSM44678 
                 60.63 
               
               
                   
               
            
           
         
       
     
     Lung Adenocarcinoma 
       
     
       
         
           
               
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 NIPD 
                 Independent 
               
               
                 Type of specimen 
                 Sample ID 
                 COSMIC ID 
                 method 
                 method 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 Fresh/frozen 
                 LCA1 
                 COSM459 
                 0.0245 
                 0.0261 
               
               
                   
                   
                 COSM527 
                 0.036 
                 0.0378 
               
               
                 Fresh/frozen 
                 LCA2 
                 COSM763 
                 0.1427 
                 0.1558 
               
               
                 Fresh/frozen 
                 LCA3 
                 COSM522 
                 0.3815 
                 0.3492 
               
               
                 Fresh/frozen 
                 LCA4 
                 COSM521 
                 0.106 
                 0.0923 
               
               
                 Fresh/frozen 
                 LCA6 
                 COSM3675521 
                 0.1387 
                 0.1026 
               
               
                 Fresh/frozen 
                 LCA13 
                 MET 
                 0.0126 
                 Not covered 
               
               
                   
                   
                 c.3028 + 1G &gt; T 
               
               
                 Fresh/frozen 
                 LCA15 
                 COSM27887 
                 0.1352 
                 Not covered 
               
               
                   
                   
                 COSM521 
                 0.2871 
                 0.3185 
               
               
                 Fresh/frozen 
                 LCA21 
                 COSM763 
                 0.2798 
                 0.3128 
               
               
                 FFPE 
                 LCA36 
                 COSM6224 
                 0.2431 
                 0.1847 
               
               
                 FFPE 
                 LCA40 
                 COSM6225 
                 0.08 
                 0.1148 
               
               
                 FFPE 
                 LCA45 
                 COSM6223 
                 0.2098 
                 0.2456 
               
               
                 FFPE 
                 LCA47 
                 COSM12370 
                 0.6295 
                 0.5719 
               
               
                 FFPE 
                 LCA48 
                 COSM522 
                 0.2649 
                 0.4032 
               
               
                   
               
            
           
         
       
     
     For the lung cancer data, results were compared with data obtained for the same tissue samples with an independent method. For the genomic regions covered by both methods we observed 100% concordance.