Abstract:
The present teachings provide methods for predicting the clinical outcome of the treatment of human solid tumors. In some embodiments, the method includes measuring in the cells of a tumor the expression level of a set of genes whose change is related to chromosomal instability; taking a statistical measure of the expression level of the set of measured genes; and if the statistical measure of the expression level of the set of measured genes is elevated, determining that the prognosis is poor. Another aspect of the present teachings is the sets of genes, which are useful in predicting the outcome of treatment of solid tumors.

Description:
GOVERNMENT SUPPORT 
       [0001]    The United States government has certain rights to this invention pursuant to Grant No. 1PO1CA 092644-01 from the National Cancer Institute. 
     
    
     FIELD 
       [0002]    The present teachings relate generally to the field of cancer diagnostics and treatment, and more specifically to the determination of the likelihood that the outcome of a treatment will be successful. 
       BACKGROUND 
       [0003]    The treatment options for solid human tumors are multifold. Solid tumors can be treated chemotherapeutically, radiologically, surgically, or with a combination of these therapies. Each therapy produces undesirable side effects, which may be extensive enough that some patients cannot complete the course of treatment. The side effects of cancer therapy also have a severe impact on the quality of life of these patients. 
         [0004]    As a result, if the clinician can determine prior to treatment how refractory the tumor will respond to treatment, an appropriate treatment can be selected having the least side effects for the patient. The present teachings provide a method for determining likelihood of clinical outcome based on the malignancy of the tumor. 
       SUMMARY 
       [0005]    The present teachings relate to methods for predicting the outcome of the treatment of solid human tumors. In various embodiments, the methods generally include measuring in a particular solid tumor cancer type the degree of chromosomal abnormalities and/or the expression levels of a large number of genes; identifying a subset of the measured genes characteristic of chromosomal instability (CIN); and determining in clinical samples whether the CIN signature accurately predicts the outcome of the treatment of the solid tumor. The methods can include the use of the CIN signature to analyze a tumor of a patient to determine the prognosis of the cancer and whether treatment is likely to be successful. 
         [0006]    In certain embodiments, the method comprises measuring in solid tumor cells the mRNA expression of at least 25 genes in the following set of genes: 
         [0000]                                    1   TPX2       2   PRC1       3   FOXM1       4   CDC2       5   C20orf24/TGIF2       6   MCM2       7   H2AFZ       8   TOP2A       9   PCNA       10   UBE2C       11   MELK       12   TRIP13       13   CNAP1       14   MCM7       15   RNASEH2A       16   RAD51AP1       17   KIF20A       18   CDC45L       19   MAD2L1       20   ESPL1       21   CCNB2       22   FEN1       23   TTK       24   CCT5       25   RFC4       26   ATAD2       27   ch-TOG       28   NUP205       29   CDC20       30   CKS2       31   RRM2       32   ELAVL1       33   CCNB1       34   RRM1       35   AURKB       36   MSH6       37   EZH2       38   CTPS       39   DKC1       40   OIP5       41   CDCA8       42   PTTG1       43   C10 or f3       44   H2AFX       45   CMAS       46   BRRN1       47   MCM10       48   LSM4       49   MTB       50   ASF1B       51   ZWINT       52   TOPK       53   FLJ10036       54   CDCA3       55   ECT2       56   CDC6       57   UNG       58   MTCH2       59   RAD21       60   ACTL6A       61   GPI/MGC13096       62   SFRS2       63   HDGF       64   NXT1       65   NEK2       66   DHCR7       67   STK6       68   NDUFAB1       69   KIAA0286       70   KIF4A       71   SNRPB/GC10715       72   UCK2       73   PARP1       74   RAD54L       75   NUSAP1       76   RFC5       77   TK1       78   WBP11       79   SYNCRIP/SNX14       80   BIRC5/AFMID       81   HNRPAB       82   TACC3       83   MKI67       84   CENPF       85   Spc25       86   C20 or f172       87   PTBP1       88   DLG7       89   POLR2K       90   IARS       91   HPRT1       92   NSDHL       93   KNTC2       94   RAMP       95   C10 or f7       96   C12 or f14       97   SNRPD1       98   FLJ20989       99   NIF3L1       100   DER1                    
taking a statistical measure of the expression level of the measured genes; and if the statistical measure of the expression level of the measured genes is elevated, determining, to a 99% confidence level, that the prognosis is poor. It should be understood that the other gene sets described herein are equally applicable to the above described method.
 
         [0007]    In certain embodiments, the solid tumor is of a cancer selected from lung cancer, prostate cancer, medulloblastoma, glioma, breast cancer, and lymphoma. 
         [0008]    In some embodiments, the statistical measure of the expression level of the measured genes is a linear combination of the expression level of the genes in the set of genes. In particular embodiments, the linear combination of the expression level in the set of genes is a combination of weighted expression levels. In various embodiments, the linear combination of the expression level in the set of genes is the mean of the logarithm of each of the expression levels. In certain embodiments, the statistical measure of the expression level of the measured genes is elevated relative to the expression level of the measured genes from a tumor whose prognosis is good. 
         [0009]    In some embodiments, the present teachings relate to a method for predicting outcome of the treatment of the human solid tumors. In these embodiments, the method generally includes the steps of measuring in the cells of a tumor the expression level of a set of genes (or subset of a gene set) whose change is related to chromosomal instability; taking a statistical measure of the expression level of the set of measured genes; and if the statistical measure of the expression level of the set of measured genes is elevated, determining that the prognosis is poor. In various embodiments, chromosomal instability can be measured by array comparative genomic hybridization (aCGH) and/or counting the number of morphologically visible chromosomal aberrations by the application of chromosome visualization methods such as spectral karyotyping (SKY). Such techniques can be used in conjunction with expression levels or to correlate and/or corroborate expression levels. 
         [0010]    Another aspect of the present teachings is a set of genes or data from a set of genes, e.g., expression level data, useful in determining the outcome of treatment of solid tumors. In some embodiments, the set of genes comprises or consists essentially of: 
         [0000]    
       
         
               
               
             
               
             
               
               
             
               
             
               
               
             
               
             
               
               
             
           
               
                   
               
             
             
               
                 1 
                 TPX2 
               
               
                 2 
                 PRC1 
               
               
                 3 
                 FOXM1 
               
               
                 4 
                 CDC2 
               
               
                 5 
                 C20 or f24/TGIF2 
               
               
                 6 
                 MCM2 
               
               
                 7 
                 H2AFZ 
               
               
                 8 
                 TOP2A 
               
               
                 9 
                 PCNA 
               
               
                 10 
                 UBE2C 
               
               
                 11 
                 MELK 
               
               
                 12 
                 TRIP13 
               
               
                 13 
                 CNAP1 
               
               
                 14 
                 MCM7 
               
               
                 15 
                 RNASEH2A 
               
               
                 16 
                 RAD51AP1 
               
               
                 17 
                 KIF20A 
               
               
                 18 
                 CDC45L 
               
               
                 19 
                 MAD2L1 
               
               
                 20 
                 ESPL1 
               
               
                 21 
                 CCNB2 
               
               
                 22 
                 FEN1 
               
               
                 23 
                 TTK 
               
               
                 24 
                 CCT5 
               
               
                 25 
                 RFC4 
               
               
                 26 
                 ATAD2 
               
               
                 27 
                 ch-TOG 
               
               
                 28 
                 NUP205 
               
               
                 29 
                 CDC20 
               
               
                 30 
                 CKS2 
               
               
                 31 
                 RRM2 
               
               
                 32 
                 ELAVL1 
               
               
                 33 
                 CCNB1 
               
               
                 34 
                 RRM1 
               
               
                 35 
                 AURKB 
               
               
                 36 
                 MSH6 
               
               
                 37 
                 EZH2 
               
               
                 38 
                 CTPS 
               
               
                 39 
                 DKC1 
               
               
                 40 
                 OIP5 
               
               
                 41 
                 CDCA8 
               
               
                 42 
                 PTTG1 
               
               
                 43 
                 C10orf3/CEP55 
               
               
                 44 
                 H2AFX 
               
               
                 45 
                 CMAS 
               
               
                 46 
                 BRRN1 
               
               
                 47 
                 MCM10 
               
               
                 48 
                 LSM4 
               
               
                 49 
                 MTB 
               
               
                 50 
                 ASF1B 
               
               
                 51 
                 ZWINT 
               
               
                 52 
                 TOPK 
               
               
                 53 
                 FLJ10036 
               
               
                 54 
                 CDCA3 
               
               
                 55 
                 ECT2 
               
               
                 56 
                 CDC6 
               
               
                 57 
                 UNG 
               
               
                 58 
                 MTCH2 
               
               
                 59 
                 RAD21 
               
               
                 60 
                 ACTL6A 
               
               
                 61 
                 GPI and MGC13096 
               
               
                 62 
                 SFRS2 
               
               
                 63 
                 HDGF 
               
               
                 64 
                 NXT1 
               
               
                 65 
                 NEK2 
               
               
                 66 
                 DHCR7 
               
               
                 67 
                 STK6 
               
               
                 68 
                 NDUFAB1 
               
               
                 69 
                 KIAA0286 
               
               
                 70 
                 KIF4A 
               
               
                 71 
                 SNRPB/MGC10715 
               
               
                 72 
                 UCK2 
               
               
                 73 
                 PARP1 
               
               
                 74 
                 RAD54L 
               
               
                 75 
                 NUSAP1 
               
               
                 76 
                 RFC5 
               
               
                 77 
                 TK1 
               
               
                 78 
                 WBP11 
               
               
                 79 
                 SYNCRIP/SNX14 
               
               
                 80 
                 BIRC5 and AFMID 
               
               
                 81 
                 HNRPAB 
               
               
                 82 
                 TACC3 
               
               
                 83 
                 MKI67 
               
               
                 84 
                 CENPF 
               
               
                 85 
                 Spc25 
               
               
                 86 
                 C20 or f172 
               
               
                 87 
                 PTBP1 
               
               
                 88 
                 DLG7 
               
               
                 89 
                 POLR2K 
               
               
                 90 
                 IARS 
               
               
                 91 
                 HPRT1 
               
               
                 92 
                 NSDHL 
               
               
                 93 
                 KNTC2 
               
               
                 94 
                 RAMP 
               
               
                 95 
                 C10 or f7 
               
               
                 96 
                 C12 or f14 
               
               
                 97 
                 SNRPD1 
               
               
                 98 
                 FLJ20989 
               
               
                 99 
                 NIF3L1 
               
               
                 100 
                 DER1 
               
             
          
           
               
                 or 
               
             
          
           
               
                 1 
                 TPX2 
               
               
                 2 
                 PRC1 
               
               
                 3 
                 FOXM1 
               
               
                 4 
                 CDC2 
               
               
                 5 
                 C20 or f24/TGIF2 
               
               
                 6 
                 MCM2 
               
               
                 7 
                 H2AFZ 
               
               
                 8 
                 TOP2A 
               
               
                 9 
                 PCNA 
               
               
                 10 
                 UBE2C 
               
               
                 11 
                 MELK 
               
               
                 12 
                 TRIP13 
               
               
                 13 
                 CNAP1 
               
               
                 14 
                 MCM7 
               
               
                 15 
                 RNASEH2A 
               
               
                 16 
                 RAD51AP1 
               
               
                 17 
                 KIF20A 
               
               
                 18 
                 CDC45L 
               
               
                 19 
                 MAD2L1 
               
               
                 20 
                 ESPL1 
               
               
                 21 
                 CCNB2 
               
               
                 22 
                 FEN1 
               
               
                 23 
                 TTK 
               
               
                 24 
                 CCT5 
               
               
                 25 
                 RFC4 
               
               
                 26 
                 ATAD2 
               
               
                 27 
                 ch-TOG 
               
               
                 28 
                 NUP205 
               
               
                 29 
                 CDC20 
               
               
                 30 
                 CKS2 
               
               
                 31 
                 RRM2 
               
               
                 32 
                 ELAVL1 
               
               
                 33 
                 CCNB1 
               
               
                 34 
                 RRM1 
               
               
                 35 
                 AURKB 
               
               
                 36 
                 MSH6 
               
               
                 37 
                 EZH2 
               
               
                 38 
                 CTPS 
               
               
                 39 
                 DKC1 
               
               
                 40 
                 OIP5 
               
               
                 41 
                 CDCA8 
               
               
                 42 
                 PTTG1 
               
               
                 43 
                 CEP55/C10orf3 
               
               
                 44 
                 H2AFX 
               
               
                 45 
                 CMAS 
               
               
                 46 
                 BRRN1 
               
               
                 47 
                 MCM10 
               
               
                 48 
                 LSM4 
               
               
                 49 
                 MTB 
               
               
                 50 
                 ASF1B 
               
               
                 51 
                 ZWINT 
               
               
                 52 
                 TOPK 
               
               
                 53 
                 FLJ10036 
               
               
                 54 
                 CDCA3 
               
               
                 55 
                 ECT2 
               
               
                 56 
                 CDC6 
               
               
                 57 
                 UNG 
               
               
                 58 
                 MTCH2 
               
               
                 59 
                 RAD21 
               
               
                 60 
                 ACTL6A 
               
               
                 61 
                 GPI/MGC13096 
               
               
                 62 
                 SFRS2 
               
               
                 63 
                 HDGF 
               
               
                 64 
                 NXT1 
               
               
                 65 
                 NEK2 
               
               
                 66 
                 DHCR7 
               
               
                 67 
                 STK6 
               
               
                 68 
                 NDUFAB1 
               
               
                 69 
                 KIAA0286 
               
               
                 70 
                 KIF4A 
               
             
          
           
               
                 or 
               
             
          
           
               
                 1 
                 TPX2 
               
               
                 2 
                 PRC1 
               
               
                 3 
                 FOXM1 
               
               
                 4 
                 CDC2 
               
               
                 5 
                 C20 or f24/TGIF2 
               
               
                 6 
                 MCM2 
               
               
                 7 
                 H2AFZ 
               
               
                 8 
                 TOP2A 
               
               
                 9 
                 PCNA 
               
               
                 10 
                 UBE2C 
               
               
                 11 
                 MELK 
               
               
                 12 
                 TRIP13 
               
               
                 13 
                 CNAP1 
               
               
                 14 
                 MCM7 
               
               
                 15 
                 RNASEH2A 
               
               
                 16 
                 RAD51AP1 
               
               
                 17 
                 KIF20A 
               
               
                 18 
                 CDC45L 
               
               
                 19 
                 MAD2L1 
               
               
                 20 
                 ESPL1 
               
               
                 21 
                 CCNB2 
               
               
                 22 
                 FEN1 
               
               
                 23 
                 TTK 
               
               
                 24 
                 CCT5 
               
               
                 25 
                 RFC4 
               
             
          
           
               
                 or 
               
             
          
           
               
                 1 
                 TPX2 
               
               
                 2 
                 FOXM1 
               
               
                 3 
                 CDC2 
               
               
                 4 
                 MCM2 
               
               
                 5 
                 H2AFZ 
               
               
                 6 
                 TOP2A 
               
               
                 7 
                 PCNA 
               
               
                 8 
                 UBE2C 
               
               
                 9 
                 MELK 
               
               
                 10 
                 TRIP13 
               
               
                 11 
                 MCM7 
               
               
                 12 
                 CDC45L 
               
               
                 13 
                 MAD2L1 
               
               
                 14 
                 ESPL1 
               
               
                 15 
                 CCNB2 
               
               
                 16 
                 FEN1 
               
               
                 17 
                 TTK 
               
               
                 18 
                 CCT5 
               
               
                 19 
                 RFC4 
               
               
                 20 
                 ch-TOG 
               
               
                 21 
                 NUP205 
               
               
                 22 
                 CDC20 
               
               
                 23 
                 CKS2 
               
               
                 24 
                 CCNB1 
               
               
                 25 
                 AURKB 
               
               
                 26 
                 MSH6 
               
               
                 27 
                 EZH2 
               
               
                 28 
                 OIP5 
               
               
                 29 
                 PTTG1 
               
               
                 30 
                 H2AFX 
               
               
                 31 
                 ZWINT 
               
               
                 32 
                 CDC6 
               
               
                 33 
                 UNG 
               
               
                 34 
                 RAD21 
               
               
                 35 
                 ACTL6A 
               
               
                 36 
                 DHCR7 
               
               
                 37 
                 STK6 
               
               
                 38 
                 KIAA0286 
               
               
                 39 
                 SNRPB/MGC10715 
               
               
                 40 
                 TK1 
               
               
                 41 
                 HNRPAB 
               
               
                 42 
                 MKI67 
               
               
                 43 
                 CENPF 
               
               
                 44 
                 Spc25 
               
               
                 45 
                 DLG7 
               
               
                 46 
                 HPRT1 
               
               
                 47 
                 KNTC2 
               
               
                 48 
                 MSH2 
               
               
                 49 
                 NUP155 
               
               
                 50 
                 POP7 
               
               
                 51 
                 LMNB1 
               
               
                 52 
                 CDKN3 
               
               
                 53 
                 LRP8 
               
               
                 54 
                 TYMS 
               
               
                 55 
                 CCNA2 
               
               
                 56 
                 MTHFD2 
               
               
                 57 
                 RFC2 
               
               
                 58 
                 MCM6 
               
               
                 59 
                 FANCG 
               
               
                 60 
                 MYBL2 
               
               
                 61 
                 MCM3 
               
               
                 62 
                 NCOA6 
               
               
                 63 
                 EIF2C2 
               
               
                 64 
                 TROAP 
               
               
                 65 
                 SIL 
               
               
                 66 
                 PRIM1 
               
               
                 67 
                 POLD2 
               
               
                 68 
                 EST1B 
               
               
                 69 
                 GGH 
               
               
                   
               
             
          
         
       
     
         [0011]    Data derived from a set of genes can include the expression level measurement of each of the genes in the set or for a subset of genes in a gene set as well as other measurements related to the genes as described herein. The data of the other measurements can be independent of the expression levels. Further, such data can be contained on a computer readable medium. 
         [0012]    The foregoing, and other features and advantages of the present teachings, will be more fully understood from the following description and claims. 
     
    
     DETAILED DESCRIPTION 
       [0013]    Throughout the description, where compositions are described as having, including, or comprising specific components, or where processes are described as having, including, or comprising specific process steps, it is contemplated that compositions of the present teachings also consist essentially of, or consist of, the recited components, and that the processes of the present teachings also consist essentially of, or consist of, the recited processing steps. 
         [0014]    In the application, where an element or component is said to be included in and/or selected from a list of recited elements or components, it should be understood that the element or component can be any one of the recited elements or components and can be selected from a group consisting of two or more of the recited elements or components. 
         [0015]    The use of the singular herein includes the plural (and vice versa) unless specifically stated otherwise. In addition, where the use of the term “about” is before a quantitative value, the present teachings also include the specific quantitative value itself, unless specifically stated otherwise. 
         [0016]    It should be understood that the order of steps or order for performing certain actions is immaterial so long as the present teachings remain operable. Moreover, two or more steps or actions can be conducted simultaneously. 
         [0017]    Human solid tumors exhibit differences in outcome even for the same tumor type. Thus, if a clinician can determine which outcome is probable for a specific tumor, the clinician would know if a more or less aggressive treatment regimen can be used. One possibility is to consider the amount of chromosomal aberrations that exists in the specific tumor. It is known for those trained in the art that there is a strong correlation between the total number of chromosomal aberrations in a given tumor and its malignancy. High numbers of chromosomal aberrations are usually associated with a more malignant phenotype. 
         [0018]    With respect to the chromosomal complement of a solid human tumor, the tumor exhibits various aberrations such as multiple trisomies, tetrasomy, and multiple translocations and deletions. These aberrations in chromosomal stability are found in solid tumors of the lung, prostate, breast, brain (both medulloblastoma and glioma), and lymph nodes (lymphoma). To quantify the amount of chromosomal aberrations, one may apply any of the following three methods: 1) counting the number of morphologically visible chromosomal aberrations by the application chromosome visualization methods such as spectral karyotyping; 2) quantifying the amount of chromosomal aberrations obtained by array comparative genomic hybridization (aCGH); and 3) quantifying chromosomal aberrations by their effect on the expression level of the genes contained in a given chromosomal region. The latter method, which is an integral part of the present teachings, produces a measure called “functional aneuploidy.” 
         [0019]    The numerical and structural chromosomal aberrations seen in malignancies are a consequence of the aberrant functioning of the cell&#39;s mechanism to maintain genomic integrity. This cellular aberration is called “chromosomal instability” (CIN). Similarly to aneuploidy, its causative mechanism, CIN is also associated with malignancies. High levels of CIN are expected to confer a more malignant phenotype. Despite the obvious utility of quantifying CIN for clinical diagnostics, its application has been hindered by technical difficulties. The current patent application provides a readily applicable quantification method of CIN in clinical tumor samples. 
         [0020]    A gene expression signature of CIN is derived by the identification of genes with the highest level of correlation between a gene&#39;s expression level and the overall level of chromosomal aberrations across a given set of cancer samples. 
         [0021]    The overall level of chromosomal aberrations in a given clinical sample can be derived by any of the three techniques described herein. 
         [0022]    In cancer cells chromosomes can be visualized by spectral karyotyping (SKY) that allows counting the total number of chromosomes and morphological aberrations of chromosomes such as deletions, insertions, translocations, and inversions of various chromosomal regions. In one embodiment the total number of such numerical and morphological aberrations in a cancer cell is used to estimate the overall level of chromosomal aberrations. 
         [0023]    In cancer cells the copy number of each chromosomal region can be measured by array comparative genomic hybridization using microarrays by containing either long cDNA clones targeting the individual chromosomal regions or short DNA probes, such as those used on the so-called single nucleotide polymorphism (SNP) chips. In one embodiment the total number of chromosomal aberrations in a cancer sample is calculated by adding up the deviation of each chromosomal region from the normal chromosomal copy number across the entire genome. 
         [0024]    In cancer cells chromosomal copy number changes have a direct impact on the RNA expression level of the genes contained in a given chromosomal region. Therefore, chromosomal copy number changes can be estimated by calculating the net deviation of the expression level of all genes contained in a given chromosomal region relative to the remainder of the sampled transcriptome. 
         [0025]    First a tumor sample from each of the solid tumors of interest was obtained. A microarray was then used to quantify the expression level of a large number, typically 10,000-20,000 genes in each tumor sample. For a given microarray, each probe or probe set was first mapped to its corresponding transcriptome by sequence mapping and then, through this transcript, the microarray probes were mapped to their respective chromosomal cytobands. 
         [0026]    For each chromosomal cytoband, all of the genes present in the microarray measurement that map to that region are grouped into a set designated B (short for band). In one embodiment, if less than ten genes were mapped to a band, the group was disregarded as statistically unreliable. Although in this embodiment the mapping of genes to the cytobands of the chromosome was used to group the genes, it is contemplated that the grouping of genes into statistically meaningful sets can be accomplished by using windows of equal linear length along the chromosome (5-30 Mb long) or genes can be grouped by neighborhood criteria (20 to 100 genes that are located next to each other on the same chromosome would form a set of genes for further analysis). Also, although ten genes were considered the minimum number of genes necessary to form a group, it is contemplated that other numbers of genes can be used to determine statistical reliability. 
         [0027]    The rest of the genes, i.e. the rest of the transcriptome that is localized somewhere else on the chromosomes and which are measured on the same microarray, are grouped into a set G (short for genome). The sets B and G are disjoint. The distributions of the genes in B and G are then compared using an appropriate statistical metric, such as the t-statistic. In one embodiment, the statistical significance of the group of genes was determined by taking the mean of the log to the base ten of the expression level of each gene in the group B and comparing it with the expression level of the genes from group G. In general, the statistical metric is formed on a linear combination of the expression level of the genes in the set of genes. The expression levels can be weighted. Other statistical tests, which can be used include: Wilcoxon-Rank test, Signal to Noise ratio, Kolmogorov-Smirnov test and Kruskal-Wallis test 
         [0028]    This process is iterated for each gene expression profile in a given cohort such that upon termination, a matrix of t-statistics for each of approximately 350 cytobands per hybridization was obtained. The thus created statistical measures will provide an estimate of the level of aberrant gene expression of a given gene set contained within a given chromosomal region. This is a basis of functional aneuploidy, a measure of the impact of chromosomal aberrations on the transcriptome. 
         [0029]    In addition to the measures outlined above, the overall level of chromosomal aberrations can be characterized by summing up the level of functional aneuploidy across all chromosomal regions. This novel measure is termed total functional aneuploidy. 
         [0030]    For a given set of cancer samples the following measures are obtained: (a) gene expression measurements at the RNA level for typically 10,000-20,000 genes, usually but not exclusively obtained by microarray measurements. This is a key for all subsequent steps. In addition to this the following measures may also be obtained (b) array comparative genomic hybridization across the entire genome and/or (c) a detailed morphological characterization of all chromosomal aberrations. 
         [0031]    For each gene in a given cancer data the gene&#39;s expression level across all samples will form a gene expression vector. The total number of chromosomal aberrations in the individual cancer samples as determined by the total number of morphological aberrations, total number of aCGH based chromosomal copy number deviations and total functional aneuploidy will form three additional vectors. Correlation between each gene expression vector and the three vectors characterizing the overall level of chromosomal aberrations is calculated for all genes. The genes with the highest level of correlation to the overall level of chromosomal aberrations will form the CIN gene expression signature. 
         [0032]    A group of expressed genes in a tumor which was difficult to treat showed increased expression relative to tumors which were easier to treat. These genes included: 
         [0000]    
       
         
               
               
             
           
               
                   
               
             
             
               
                 1 
                 TPX2 
               
               
                 2 
                 PRC1 
               
               
                 3 
                 FOXM1 
               
               
                 4 
                 CDC2 
               
               
                 5 
                 C20 or f24/TGIF2 
               
               
                 6 
                 MCM2 
               
               
                 7 
                 H2AFZ 
               
               
                 8 
                 TOP2A 
               
               
                 9 
                 PCNA 
               
               
                 10 
                 UBE2C 
               
               
                 11 
                 MELK 
               
               
                 12 
                 TRIP13 
               
               
                 13 
                 CNAP1 
               
               
                 14 
                 MCM7 
               
               
                 15 
                 RNASEH2A 
               
               
                 16 
                 RAD51AP1 
               
               
                 17 
                 KIF20A 
               
               
                 18 
                 CDC45L 
               
               
                 19 
                 MAD2L1 
               
               
                 20 
                 ESPL1 
               
               
                 21 
                 CCNB2 
               
               
                 22 
                 FEN1 
               
               
                 23 
                 TTK 
               
               
                 24 
                 CCT5 
               
               
                 25 
                 RFC4 
               
               
                 26 
                 ATAD2 
               
               
                 27 
                 ch-TOG 
               
               
                 28 
                 NUP205 
               
               
                 29 
                 CDC20 
               
               
                 30 
                 CKS2 
               
               
                 31 
                 RRM2 
               
               
                 32 
                 ELAVL1 
               
               
                 33 
                 CCNB1 
               
               
                 34 
                 RRM1 
               
               
                 35 
                 AURKB 
               
               
                 36 
                 MSH6 
               
               
                 37 
                 EZH2 
               
               
                 38 
                 CTPS 
               
               
                 39 
                 DKC1 
               
               
                 40 
                 OIP5 
               
               
                 41 
                 CDCA8 
               
               
                 42 
                 PTTG1 
               
               
                 43 
                 C10orf3 
               
               
                 44 
                 H2AFX 
               
               
                 45 
                 CMAS 
               
               
                 46 
                 BRRN1 
               
               
                 47 
                 MCM10 
               
               
                 48 
                 LSM4 
               
               
                 49 
                 MTB 
               
               
                 50 
                 ASF1B 
               
               
                 51 
                 ZWINT 
               
               
                 52 
                 TOPK 
               
               
                 53 
                 FLJ10036 
               
               
                 54 
                 CDCA3 
               
               
                 55 
                 ECT2 
               
               
                 56 
                 CDC6 
               
               
                 57 
                 UNG 
               
               
                 58 
                 MTCH2 
               
               
                 59 
                 RAD21 
               
               
                 60 
                 ACTL6A 
               
               
                 61 
                 GPI and MGC13096 
               
               
                 62 
                 SFRS2 
               
               
                 63 
                 HDGF 
               
               
                 64 
                 NXT1 
               
               
                 65 
                 NEK2 
               
               
                 66 
                 DHCR7 
               
               
                 67 
                 STK6 
               
               
                 68 
                 NDUFAB1 
               
               
                 69 
                 KIAA0286 
               
               
                 70 
                 KIF4A 
               
               
                 71 
                 SNRPB/MGC10715 
               
               
                 72 
                 UCK2 
               
               
                 73 
                 PARP1 
               
               
                 74 
                 RAD54L 
               
               
                 75 
                 NUSAP1 
               
               
                 76 
                 RFC5 
               
               
                 77 
                 TK1 
               
               
                 78 
                 WBP11 
               
               
                 79 
                 SYNCRIP/SNX14 
               
               
                 80 
                 BIRC5 and AFMID 
               
               
                 81 
                 HNRPAB 
               
               
                 82 
                 TACC3 
               
               
                 83 
                 MKI67 
               
               
                 84 
                 CENPF 
               
               
                 85 
                 Spc25 
               
               
                 86 
                 C20orf172 
               
               
                 87 
                 PTBP1 
               
               
                 88 
                 DLG7 
               
               
                 89 
                 POLR2K 
               
               
                 90 
                 IARS 
               
               
                 91 
                 HPRT1 
               
               
                 92 
                 NSDHL 
               
               
                 93 
                 KNTC2 
               
               
                 94 
                 RAMP 
               
               
                 95 
                 C10orf7 
               
               
                 96 
                 C12orf14 
               
               
                 97 
                 SNRPD1 
               
               
                 98 
                 FLJ20989 
               
               
                 99 
                 NIF3L1 
               
               
                 100 
                 DER1 
               
               
                   
               
             
          
         
       
     
         [0033]    Many of these genes are known to be related to chromosomal stability and hence are consistent with chromosomal aberrations as a cause of the malignant phenotype. The application of the method to multiple datasets indicates that the following genes consistently have increased expression in difficult-to-treat tumors: 
         [0000]    
       
         
               
               
             
           
               
                   
               
             
             
               
                 1 
                 TPX2 
               
               
                 2 
                 FOXM1 
               
               
                 3 
                 CDC2 
               
               
                 4 
                 MCM2 
               
               
                 5 
                 H2AFZ 
               
               
                 6 
                 TOP2A 
               
               
                 7 
                 PCNA 
               
               
                 8 
                 UBE2C 
               
               
                 9 
                 MELK 
               
               
                 10 
                 TRIP13 
               
               
                 11 
                 MCM7 
               
               
                 12 
                 CDC45L 
               
               
                 13 
                 MAD2L1 
               
               
                 14 
                 ESPL1 
               
               
                 15 
                 CCNB2 
               
               
                 16 
                 FEN1 
               
               
                 17 
                 TTK 
               
               
                 18 
                 CCT5 
               
               
                 19 
                 RFC4 
               
               
                 20 
                 ch-TOG 
               
               
                 21 
                 NUP205 
               
               
                 22 
                 CDC20 
               
               
                 23 
                 CKS2 
               
               
                 24 
                 CCNB1 
               
               
                 25 
                 AURKB 
               
               
                 26 
                 MSH6 
               
               
                 27 
                 EZH2 
               
               
                 28 
                 OIP5 
               
               
                 29 
                 PTTG1 
               
               
                 30 
                 H2AFX 
               
               
                 31 
                 ZWINT 
               
               
                 32 
                 CDC6 
               
               
                 33 
                 UNG 
               
               
                 34 
                 RAD21 
               
               
                 35 
                 ACTL6A 
               
               
                 36 
                 DHCR7 
               
               
                 37 
                 STK6 
               
               
                 38 
                 KIAA0286 
               
               
                 39 
                 SNRPB and 
               
               
                   
                 MGC10715 
               
               
                 40 
                 TK1 
               
               
                 41 
                 HNRPAB 
               
               
                 42 
                 MKI67 
               
               
                 43 
                 CENPF 
               
               
                 44 
                 Spc25 
               
               
                 45 
                 DLG7 
               
               
                 46 
                 HPRT1 
               
               
                 47 
                 KNTC2 
               
               
                 48 
                 MSH2 
               
               
                 49 
                 NUP155 
               
               
                 50 
                 POP7 
               
               
                 51 
                 LMNB1 
               
               
                 52 
                 CDKN3 
               
               
                 53 
                 LRP8 
               
               
                 54 
                 TYMS 
               
               
                 55 
                 CCNA2 
               
               
                 56 
                 MTHFD2 
               
               
                 57 
                 RFC2 
               
               
                 58 
                 MCM6 
               
               
                 59 
                 FANCG 
               
               
                 60 
                 MYBL2 
               
               
                 61 
                 MCM3 
               
               
                 62 
                 NCOA6 
               
               
                 63 
                 EIF2C2 
               
               
                 64 
                 TROAP 
               
               
                 65 
                 SIL 
               
               
                 66 
                 PRIM1 
               
               
                 67 
                 POLD2 
               
               
                 68 
                 EST1B 
               
               
                 69 
                 GGH 
               
               
                   
               
             
          
         
       
     
         [0034]    Therefore, by determining that these sets of tumor genes or an appropriate subset thereof have an elevated expression level, the clinician can determine that the tumor is difficult to treat. 
         [0035]    The present teachings encompass embodiments in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the present teachings described herein. Scope of the present invention is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein.