Patent Publication Number: US-2013244902-A1

Title: Early detection of pancreatic cancer

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of U.S. Provisional Application Serial No. 61/417,066, filed Nov. 24, 2010. The disclosure of the prior application is considered part of (and are incorporated by reference in) the disclosure of this application. 
    
    
     STATEMENT AS TO FEDERALLY SPONSORED RESEARCH 
     This invention was made with government support under grant CA102701 awarded by the National Institutes of Health. The government has certain rights in the invention. 
    
    
     BACKGROUND 
     1. Technical Field 
     This document relates to methods and materials involved in the early detection of pancreatic cancer. For example, this document provides methods and materials for assessing nucleic acid obtained from a blood sample of a human for a CpG methylation site profile that, at least in part, indicates that the human has pancreatic cancer. 
     2. Background Information 
     Pancreatic cancer (PaC) is the 10th most common tumor type for men and women in yearly incidence in the United States and the fourth leading cause of cancer mortality (Jemal et al.,  CA Cancer J. Clin.,  60(5):277-300 (2010)). PaC is associated with a very poor prognosis as it remains one of the most difficult tumors to treat. Much of this may be attributed to the late stage at which cancer is usually detected. Between 1999 and 2006, only 8% of patients were diagnosed, often by incidental finding on radiologic imaging, at a localized stage where immediate surgical resection and subsequent cure could be considered. 
     SUMMARY 
     This document relates to methods and materials involved in the early detection of pancreatic cancer. For example, this document provides methods and materials for assessing nucleic acid obtained from a blood sample of a human for a CpG methylation site profile that, at least in part, indicates that the human has pancreatic cancer. 
     As described herein, nucleic acid from blood cells of humans with pancreatic cancer can contain different levels of the methylation CpG sites listed in Table 1 or 5 when compared to the level of methylation of those CpG sites in nucleic acid from blood cells of humans without pancreatic cancer. In particular, the methylation change in at least three methylation CpG sites listed in Table 1 or 5 (e.g., IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817 CpG methylation sites) can indicate that a human has pancreatic cancer. In some cases, detecting a reduction or low level of methylation of the LCN2_P86 site can indicate that the human has resectable pancreatic cancer. 
     The methods and materials provided herein can allow clinicians to detect humans with pancreatic cancer at an early stage without the need to obtain invasive tissue biopsies (e.g., pancreas tissue biopsies). Such an early detection can allow patients to be treated sooner with the hopes that a successful treatment outcome will be achieved. 
     In general, one aspect of this document features a method for identifying a human as having pancreatic cancer. The method comprises, or consists essentially of, (a) determining whether or not nucleic acid obtained from a blood sample of a human comprises at least three methylation CpG sites that have an altered methylation status indicative of pancreatic cancer, wherein the at least three methylation CpG sites are selected from the group consisting of IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817 CpG methylation sites, and (b) classifying the human as having pancreatic cancer if the nucleic acid comprises the at least three methylation CpG sites that have an altered methylation status indicative of pancreatic cancer, and classifying the human as not having pancreatic cancer if the nucleic acid does not comprise the at least three methylation CpG sites that have an altered methylation status indicative of pancreatic cancer. The blood sample can be a blood sample obtained from a human not subjected to a prior pancreas tissue biopsy. The method can comprise determining whether or not nucleic acid obtained from the blood sample comprises at least four methylation CpG sites that have an altered methylation status indicative of pancreatic cancer. The at least four methylation CpG sites can be selected from the group consisting of IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817 CpG methylation sites. The method can comprise determining whether or not nucleic acid obtained from the blood sample comprises at least five methylation CpG sites that have an altered methylation status indicative of pancreatic cancer. The at least five methylation CpG sites can be selected from the group consisting of IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817 CpG methylation sites. 
     In another aspect, this document features a method for identifying a human as having pancreatic cancer. The method comprises, or consists essentially of, (a) detecting the presence of at least three methylation CpG sites that have an altered methylation status indicative of pancreatic cancer in nucleic acid obtained from a blood sample of a human, wherein the at least three methylation CpG sites are selected from the group consisting of IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817 CpG methylation sites, and (b) classifying the human as having pancreatic cancer based at least in part on the presence of the at least three methylation CpG sites that have an altered methylation status indicative of pancreatic cancer. The blood sample can be a blood sample obtained from a human not subjected to a prior pancreas tissue biopsy. The method can comprise detecting the presence of at least four methylation CpG sites that have an altered methylation status indicative of pancreatic cancer in the nucleic acid. The at least four methylation CpG sites can be selected from the group consisting of IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817 CpG methylation sites. The method can comprise detecting the presence of at least five methylation CpG sites that have an altered methylation status indicative of pancreatic cancer in the nucleic acid. The at least five methylation CpG sites can be selected from the group consisting of IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817 CpG methylation sites. 
     In another aspect, this document features a method for identifying a human as having resectable pancreatic cancer. The method comprises, or consists essentially of, (a) determining whether or not nucleic acid obtained from a blood sample of a human comprises hypomethylation of an LCN2_P86 methylation CpG site, and (b) classifying the human as having resectable pancreatic cancer if the nucleic acid comprises the hypomethylation of the LCN2_P86 methylation CpG site, and classifying the human as not having resectable pancreatic cancer if the nucleic acid does not comprise the hypomethylation of the LCN2_P86 methylation CpG site. 
     In another aspect, this document features a method for identifying a human as having resectable pancreatic cancer. The method comprises, or consists essentially of, (a) detecting hypomethylation of an LCN2_P86 methylation CpG site of nucleic acid obtained from a blood sample of a human, and (b) classifying the human as having resectable pancreatic cancer based at least in part on the hypomethylation. 
     Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. 
     The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims. 
    
    
     
       DESCRIPTION OF THE DRAWINGS 
         FIG. 1 : Methylation level agreement between phase I and phase II. Representative Bland-Altman graph in one subject demonstrates good agreement between phase I and phase II data in most 96 CpG sites. Each dot represents one CpG site. Mean methylation level for each CpG site (from 0 to 100%) is shown in x-axis. Methylation level difference for each CpG site between phase I and phase II is shown in y-axis. The dashed lines indicate 95% confidence interval for the difference between the two assays, and the solid line indicates the average differences between the two assays. 
         FIG. 2 : Validation of 96 selected CpG sites. Scatter plot shows reproducible methylation differences between phase I and phase II. Wilcoxon Rank Sum z-values were plotted on x-axis (phase I) and y-axis (phase II). 88 of the 96 CpG sites were validated by p value (&lt;0.05) and direction (hyper/hypo-methylation). Although 8 CpG sites were not statistically significant, the trends in both phases are all the same. 
     
    
    
     DETAILED DESCRIPTION 
     This document provides methods and materials involved in the early detection of pancreatic cancer. For example, this document provides methods and materials for assessing nucleic acid obtained from a blood sample of a human for a CpG methylation site profile that, at least in part, indicates that the human has pancreatic cancer. 
     As described herein, nucleic acid from blood samples of humans with pancreatic cancer can contain different levels of methylation at particular CpG sites (e.g., the methylation CpG sites listed in Table 1 or the methylation CpG sites listed in Table 5) when compared to nucleic acid from blood samples of humans without pancreatic cancer. The methylation level change in these methylated CpG sites can be used to identify humans with pancreatic cancer. For example, the methylation level changes in at least three (e.g., at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten) methylation CpG sites listed in Table 1 or Table 5 can indicate that a human has pancreatic cancer. Methylation level changes in these methylation CpG sites listed in Table 1 can indicate that a human has pancreatic cancer. In some cases, a reduction in the level of methylation at the LCN2_P86 site for a human with pancreatic cancer, as compared to the level observed in healthy humans, can indicate that the human has resectable pancreatic cancer. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Selected CpG sites. 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                 Methylation 
                   
               
               
                   
                 Gene 
                 GenBank ® 
                 GenBank ® 
                   
                 change in 
                 SEQ 
               
               
                 Illumina ID 
                 Symbol 
                 Accession No. 
                 GI No. 
                 Sequence of CpG region 
                 cancer patients 
                 ID NO: 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 JAK3_P1075_R 
                 JAK3 
                 NM_000215.2 
                 47157314 
                 AACAAAGAAAGCCAGGGTGTCA 
                 hypomethylation 
                  1 
               
               
                   
                   
                   
                   
                 GGACAGGCACAGACTGGAACTT 
                   
                   
               
               
                   
                   
                   
                   
                 GGACC[CG]AGGCAGGACAGGG 
                   
                   
               
               
                   
                   
                   
                   
                 AGCTGGCCAGGGAAAGGGTGCT 
                   
                   
               
               
                   
                   
                   
                   
                 CCAGGAGGAGGGCA 
                   
                   
               
               
                   
               
               
                 SLC5A5_E60_F 
                 SLC5A5 
                 NM_000453.1 
                 4507034 
                 TGAGCACAGCGCCCAGGGAGAG 
                 hypomethylation 
                  2 
               
               
                   
                   
                   
                   
                 GGACAGACAGCCGGCTGCATGG 
                   
                   
               
               
                   
                   
                   
                   
                 GACAG[CG]GAACCCAGAGTGA 
                   
                   
               
               
                   
                   
                   
                   
                 GAGGGGAGGTGGCAGGACAGAC 
                   
                   
               
               
                   
                   
                   
                   
                 AGACAGCAGGGGCG 
                   
                   
               
               
                   
               
               
                 HPN_P374_R 
                 HPN 
                 NM_182983.1 
                 33695154 
                 GGGGCAGCGGCCCCGCACCCCT 
                 hypomethylation 
                  3 
               
               
                   
                   
                   
                   
                 CCTCCTTGCTGATTTGCACACA 
                   
                   
               
               
                   
                   
                   
                   
                 TTGGC[CG]CTTCAGACACGCA 
                   
                   
               
               
                   
                   
                   
                   
                 CTTCTGGGGCCAGCCCCTCCCC 
                   
                   
               
               
                   
                   
                   
                   
                 GCCTCCTCCCTGCC 
                   
                   
               
               
                   
               
               
                 AXL_E61_F 
                 AXL 
                 NM_021913.2 
                 21536465 
                 GGAGGAATGTTTACCAGACACA 
                 hypomethylation 
                  4 
               
               
                   
                   
                   
                   
                 GAGCCCAGAGGGACAGCGCCCA 
                   
                   
               
               
                   
                   
                   
                   
                 GAGCC[CG]GATAGAGAGACAC 
                   
                   
               
               
                   
                   
                   
                   
                 GGCCTCACTGGCTCAGGACAGG 
                   
                   
               
               
                   
                   
                   
                   
                 GGGCACAGCCACCA 
                   
                   
               
               
                   
               
               
                 CEACAM1_P44_R 
                 CEACAM1 
                 NM_001712.3 
                 68161539 
                 GAGCCTCCTCCCTGGGGCCCAG 
                 hypomethylation 
                  5 
               
               
                   
                   
                   
                   
                 AGCTTTGTCTGATCATGTGTGC 
                   
                   
               
               
                   
                   
                   
                   
                 TGGGG[CG]GGGTTTGTCCAGG 
                   
                   
               
               
                   
                   
                   
                   
                 AAGCTCTGTTTCCTCTCCTCTC 
                   
                   
               
               
                   
                   
                   
                   
                 ATTCCTACCTTTGT 
                   
                   
               
               
                   
               
               
                 TIE1_E66_R 
                 TIE1 
                 NM_005424.2 
                 31543809 
                 GGCCCACAGCATCTGACCCCAG 
                 hypomethylation 
                  6 
               
               
                   
                   
                   
                   
                 GCCCAGCTCGTCCTGGCTGGCC 
                   
                   
               
               
                   
                   
                   
                   
                 TGGGT[CG]GCCTCTGGAGTAT 
                   
                   
               
               
                   
                   
                   
                   
                 GGTCTGGCGGGTGCCCCCTTTC 
                   
                   
               
               
                   
                   
                   
                   
                 TTGCTCCCCATCCT 
                   
                   
               
               
                   
               
               
                 PI3_P274_R 
                 PI3 
                 NM_002638.2 
                 31657130 
                 TGGTTTTGTAATCAAGACTGGA 
                 hypomethylation 
                  7 
               
               
                   
                   
                   
                   
                 TCTACCAGTGACTTGCTGAATA 
                   
                   
               
               
                   
                   
                   
                   
                 ACCTT[CG]GTGATTCCTTTCT 
                   
                   
               
               
                   
                   
                   
                   
                 CTTCTTGGGTCTCACTGTATTT 
                   
                   
               
               
                   
                   
                   
                   
                 CAAAACATGAAGAA 
                   
                   
               
               
                   
               
               
                 MMP9_P189_F 
                 MMP9 
                 NM_004994.2 
                 74272286 
                 GCGGTTTCCTGCGGGTCTGGGG 
                 hypomethylation 
                  8 
               
               
                   
                   
                   
                   
                 TCTTGCCTGACTTGGCAGTGGA 
                   
                   
               
               
                   
                   
                   
                   
                 GACTG[CG]GGCAGTGGAGAGA 
                   
                   
               
               
                   
                   
                   
                   
                 GGAGGAGGTGGTGTAAGCCCTT 
                   
                   
               
               
                   
                   
                   
                   
                 TCTCATGCTGGTGC 
                   
                   
               
               
                   
               
               
                 IFNGR2_P377_R 
                 IFNGR2 
                 NM_005534.2 
                 47419933 
                 TGGGAAGAGCAAAAGAAAAGCT 
                 hypomethylation 
                  9 
               
               
                   
                   
                   
                   
                 CTATGTTGCAAAACCCATTTTT 
                   
                   
               
               
                   
                   
                   
                   
                 GCTAA[CG]TGTCCAGTGGGCT 
                   
                   
               
               
                   
                   
                   
                   
                 CCCGGGACGACCTGTTTTTAAA 
                   
                   
               
               
                   
                   
                   
                   
                 TTCTTGGTCTCCCT 
                   
                   
               
               
                   
               
               
                 HIC_1_SEQ_48_S103_R 
                 HIC1 
                 NM_006497.2 
                 61676185 
                 CCCCCGGCCGCCCCGACGGGCC 
                 hypomethylation 
                 10 
               
               
                   
                   
                   
                   
                 TAGTCTCCTCTATCGCTGGATG 
                   
                   
               
               
                   
                   
                   
                   
                 AAGCA[CG]AGCCGGGCCTGGG 
                   
                   
               
               
                   
                   
                   
                   
                 TAGCTATGGCGACGAGCTGGGC 
                   
                   
               
               
                   
                   
                   
                   
                 CGGGAGCGCGGCTC 
                   
                   
               
               
                   
               
               
                 MPL_P62_F 
                 MPL 
                 NM_005373.1 
                 4885490 
                 CCCCAGTGTGGTCTGGATGGGC 
                 hypomethylation 
                 11 
               
               
                   
                   
                   
                   
                 CCCAGAGGGGCAGGGACAGGGA 
                   
                   
               
               
                   
                   
                   
                   
                 CAGGA[CG]TGGGGCTGTATCT 
                   
                   
               
               
                   
                   
                   
                   
                 GACAGGAACCTGAGGGGCTGGC 
                   
                   
               
               
                   
                   
                   
                   
                 CTGGGAGGGGATTG 
                   
                   
               
               
                   
               
               
                 TAL1_P817_F 
                 TAL1 
                 NM_003189.1 
                 4507362 
                 GCGTGTTCGCTGGGGGTTAATG 
                 hypomethylation 
                 12 
               
               
                   
                   
                   
                   
                 TTTGCCTTATGACCAAGTCTCT 
                   
                   
               
               
                   
                   
                   
                   
                 GTGTC[CG]TGCCTCTCTCCAT 
                   
                   
               
               
                   
                   
                   
                   
                 TTTCTCTTCCTACCTCAAACCC 
                   
                   
               
               
                   
                   
                   
                   
                 AGCAACTTAGAAAA 
                   
                   
               
               
                   
               
               
                 DHCR24_P652_R 
                 DHCR24 
                 NM_014762.2 
                 56790943 
                 GGCTGGCACTCTTCCTCTTTTT 
                 hypomethylation 
                 13 
               
               
                   
                   
                   
                   
                 CCAGTTCACTGAGGCAGATGGG 
                   
                   
               
               
                   
                   
                   
                   
                 AGGCC[CG]GAGGAGAAAGAAT 
                   
                   
               
               
                   
                   
                   
                   
                 GAAGGAAGGCATTTCAGCCCGA 
                   
                   
               
               
                   
                   
                   
                   
                 GTAAACTCCCCAGG 
                   
                   
               
               
                   
               
               
                 EPHA2_P203_F 
                 EPHA2 
                 NM_004431.2 
                 32967310 
                 TGGACTCGCGGGCTCCCCGCAG 
                 hypomethylation 
                 14 
               
               
                   
                   
                   
                   
                 GCCTTCCAAAGTTTGAGCGTCT 
                   
                   
               
               
                   
                   
                   
                   
                 CAAAG[CG]CCAGCGCCCCTAC 
                   
                   
               
               
                   
                   
                   
                   
                 GGATTAGCCCCCAGGGATCTCT 
                   
                   
               
               
                   
                   
                   
                   
                 GAGCCTGGTATCCT 
                   
                   
               
               
                   
               
               
                 GFI1_P208_R 
                 GFI1 
                 NM_005263.2 
                 71037376 
                 ACGCGGGCTCTGCCACCGCCTG 
                 hypomethylation 
                 15 
               
               
                   
                   
                   
                   
                 AGGTCATACCCAGGCACTGGGT 
                   
                   
               
               
                   
                   
                   
                   
                 GTTGG[CG]GGAGCAGTAAAGC 
                   
                   
               
               
                   
                   
                   
                   
                 GCCATAAAAGCACCACTTGGAT 
                   
                   
               
               
                   
                   
                   
                   
                 GACTATTGCAAAGT 
                   
                   
               
               
                   
               
               
                 GSTM2_P453_R 
                 GSTM2 
                 NM_000848.2 
                 23065549 
                 GATAAGTGACAGTGAGTTATAA 
                 hypomethylation 
                 16 
               
               
                   
                   
                   
                   
                 TCATCCTTGCCTGTGTTGTCCT 
                   
                   
               
               
                   
                   
                   
                   
                 TCCCA[CG]TTAGGTCTGTCAT 
                   
                   
               
               
                   
                   
                   
                   
                 GCCACGTATGTCCGCAGTTTAT 
                   
                   
               
               
                   
                   
                   
                   
                 AACAATCTCTATCA 
                   
                   
               
               
                   
               
               
                 AIM2_E208_F 
                 AIM2 
                 NM_004833.1 
                 4757733 
                 TCGTCTCTAACCCAGCTCCTCT 
                 hypermethylation 
                 17 
               
               
                   
                   
                   
                   
                 ATGGTGCTTACCTCCTGATCCC 
                   
                   
               
               
                   
                   
                   
                   
                 TGGGG[CG]ATCAGCAAACCGG 
                   
                   
               
               
                   
                   
                   
                   
                 GTCTGCCACCTTCTTTTCAGAG 
                   
                   
               
               
                   
                   
                   
                   
                 AGCTTAACTAGCAG 
                   
                   
               
               
                   
               
               
                 AIM2_P624_F 
                 AIM2 
                 NM_004833.1 
                 4757733 
                 TGATATTAAGGGCATAATGAAG 
                 hypomethylation 
                 18 
               
               
                   
                   
                   
                   
                 CTAAGGGTCAGCAGTCAGCCAA 
                   
                   
               
               
                   
                   
                   
                   
                 GTTTT[CG]ACCATCTTGGCTT 
                   
                   
               
               
                   
                   
                   
                   
                 TAACCAGTTGCGGCCAGTTTCT 
                   
                   
               
               
                   
                   
                   
                   
                 TCTGTGTTACATTC 
                   
                   
               
               
                   
               
               
                 IL10_P85_F 
                 IL10 
                 NM_000572.2 
                 24430216 
                 AGCTCAGGGAGGCCTCTTCATT 
                 hypomethylation 
                 19 
               
               
                   
                   
                   
                   
                 CATTAAAAAGCCACAATCAAGG 
                   
                   
               
               
                   
                   
                   
                   
                 TTTCC[CG]GCACAGGATTTTT 
                   
                   
               
               
                   
                   
                   
                   
                 TCTGCTTAGAGCTCCTCCTTCT 
                   
                   
               
               
                   
                   
                   
                   
                 CTAACCTCTCTAAT 
                   
                   
               
               
                   
               
               
                 IL10_P348_F 
                 IL10 
                 NM_000572.2 
                 24430216 
                 GAGGCCCTCAGCTGTGGGTTCT 
                 hypomethylation 
                 20 
               
               
                   
                   
                   
                   
                 CATTCGCGTGTTCCTAGGTCAC 
                   
                   
               
               
                   
                   
                   
                   
                 AGTGA[CG]TGGACAAATTGCC 
                   
                   
               
               
                   
                   
                   
                   
                 CATTCCAGAATACAATGGGATT 
                   
                   
               
               
                   
                   
                   
                   
                 GAGAAATAATTGGG 
                   
                   
               
               
                   
               
               
                 VAMP8_P241_F 
                 VAMP8 
                 NM_003761.2 
                 14043025 
                 AAAAAAAGGCTGCCCTTTCTAG 
                 hypomethylation 
                 21 
               
               
                   
                   
                   
                   
                 ATCAGGAGGTCCAGCCTCTGGA 
                   
                   
               
               
                   
                   
                   
                   
                 AACCT[CG]GAGGGCTGCTTGA 
                   
                   
               
               
                   
                   
                   
                   
                 TCTTTCTTTTCTAATTCCTGAC 
                   
                   
               
               
                   
                   
                   
                   
                 AAGTTAGAAGACCT 
                   
                   
               
               
                   
               
               
                 ZAP70_P220_R 
                 ZAP70 
                 NM_001079.3 
                 46488942 
                 ACTGCTGCCTACCCTCCGGTTC 
                 hypermethylation 
                 22 
               
               
                   
                   
                   
                   
                 CAGGTATGCAGGCTTCCTCCCT 
                   
                   
               
               
                   
                   
                   
                   
                 TCTGA[CG]GTTCCTGCTGCTG 
                   
                   
               
               
                   
                   
                   
                   
                 GAGTCGTCCTTCCTGAAACCCT 
                   
                   
               
               
                   
                   
                   
                   
                 GCCTTTGCTTAGCC 
                   
                   
               
               
                   
               
               
                 IL1RN_P93_R 
                 IL1RN 
                 NM_173843.1 
                 27894320 
                 GTCACCCTCCTGGAAACTGGGC 
                 hypermethylation 
                 23 
               
               
                   
                   
                   
                   
                 CTGCTTGGCATCAAGTCAGCCA 
                   
                   
               
               
                   
                   
                   
                   
                 TCAGC[CG]GCCCATCTCCTCA 
                   
                   
               
               
                   
                   
                   
                   
                 TGCTGGCCAACCCTCTGTGAGT 
                   
                   
               
               
                   
                   
                   
                   
                 GTGTGGGAGGGGAG 
                   
                   
               
               
                   
               
               
                 PADI4_P1011_R 
                 PADI4 
                 NM_012387.1 
                 6912575 
                 CCCAGGTGCAACCACAGCTCTG 
                 hypermethylation 
                 24 
               
               
                   
                   
                   
                   
                 AGGCCACATGGGCATCCCCCTG 
                   
                   
               
               
                   
                   
                   
                   
                 GCAGG[CG]TGGCCCACACCTG 
                   
                   
               
               
                   
                   
                   
                   
                 CACTGTCTGGTCTGACACCCAG 
                   
                   
               
               
                   
                   
                   
                   
                 AGGCCCTGGCAAGA 
                   
                   
               
               
                   
               
               
                 ERCC3_P1210_R 
                 ERCC3 
                 NM_000122.1 
                 4557562 
                 TCTTGAAGAGCCTTGGTAGAAG 
                 hypomethylation 
                 25 
               
               
                   
                   
                   
                   
                 TATGGGCATTAAAGGTGATTCT 
                   
                   
               
               
                   
                   
                   
                   
                 GGTGA[CG]GCTCAGATGGAAA 
                   
                   
               
               
                   
                   
                   
                   
                 GGAGAAATATGTTATTGAAACT 
                   
                   
               
               
                   
                   
                   
                   
                 GGAGGCAAGTGGTA 
                   
                   
               
               
                   
               
               
                 CASP10_P334_F 
                 CASP10 
                 NM_001230.3 
                 47078266 
                 TCGCTCCATTGTTTATTTGCAT 
                 hypomethylation 
                 26 
               
               
                   
                   
                   
                   
                 GTGGACATAAGAAAGGGTTAAC 
                   
                   
               
               
                   
                   
                   
                   
                 ATGGC[CG]ACAACTATTTCAT 
                   
                   
               
               
                   
                   
                   
                   
                 GAGCTTTTTGGCTTTATTTGAA 
                   
                   
               
               
                   
                   
                   
                   
                 AAGTGAAGTGTGTT 
                   
                   
               
               
                   
               
               
                 CTLA4_E176_R 
                 CTLA4 
                 NM_005214.2 
                 21361211 
                 AAGACCTGAACACCGCTCCCAT 
                 hypermethylation 
                 27 
               
               
                   
                   
                   
                   
                 AAAGCCATGGCTTGCCTTGGAT 
                   
                   
               
               
                   
                   
                   
                   
                 TTCAG[CG]GCACAAGGCTCAG 
                   
                   
               
               
                   
                   
                   
                   
                 CTGAACCTGGCTACCAGGACCT 
                   
                   
               
               
                   
                   
                   
                   
                 GGCCCTGCACTCTC 
                   
                   
               
               
                   
               
               
                 IGFBP5_P9_R 
                 IGFBP5 
                 NM_000599.2 
                 46094066 
                 TTCCTAGCTCTTTTCCCCTGCA 
                 hypomethylation 
                 28 
               
               
                   
                   
                   
                   
                 GAAGTTTCCAAAGAGACTACGG 
                   
                   
               
               
                   
                   
                   
                   
                 GGCTC[CG]GGAGAGCAGGCGC 
                   
                   
               
               
                   
                   
                   
                   
                 TTTTAAATAGCCGGCCCCTGGC 
                   
                   
               
               
                   
                   
                   
                   
                 TGCCAGCCAGTTTG 
                   
                   
               
               
                   
               
               
                 AGXT_P180_F 
                 AGXT 
                 NM_000030.1 
                 4557288 
                 AAGAAACACTTCTCTCACCCCT 
                 hypomethylation 
                 29 
               
               
                   
                   
                   
                   
                 GAGCTAAGCAGAATAAGAGGGG 
                   
                   
               
               
                   
                   
                   
                   
                 CTGGA[CG]TGCAGGACTCAGA 
                   
                   
               
               
                   
                   
                   
                   
                 GTGGGAGCGAGGAGGGCTGGGG 
                   
                   
               
               
                   
                   
                   
                   
                 TGAGGACAGCTTTG 
                   
                   
               
               
                   
               
               
                 PTHR1_P258_F 
                 PTHR1 
                 NM_000316.2 
                 39995096 
                 TAAGAGAGAGGCATGGCAGGGC 
                 hypermethylation 
                 30 
               
               
                   
                   
                   
                   
                 AAGGAGAGGACTATTGAGGCAC 
                   
                   
               
               
                   
                   
                   
                   
                 ACACA[CG]TGTCTGGCAGCCT 
                   
                   
               
               
                   
                   
                   
                   
                 GAGTGGGCCCAGTTACCTGGCA 
                   
                   
               
               
                   
                   
                   
                   
                 GGCAGACCCATGGG 
                   
                   
               
               
                   
               
               
                 ZMYND10_P329__F 
                 ZMYND10 
                 NM_015896.2 
                 37594443 
                 CCCGCTGCTCTTCCTCCTCCTT 
                 hypomethylation 
                 31 
               
               
                   
                   
                   
                   
                 ATGGCTTCTTGGTTCCTCTATT 
                   
                   
               
               
                   
                   
                   
                   
                 TCTCG[CG]TCCCGGCTCCACT 
                   
                   
               
               
                   
                   
                   
                   
                 AGTTGGCTCCTGAAATACTGCC 
                   
                   
               
               
                   
                   
                   
                   
                 AGGGCGCACGACTT 
                   
                   
               
               
                   
               
               
                 IL17RB_E164_R 
                 IL17RB 
                 NM_018725.2 
                 27477073 
                 CCAGCACCTCTTCCCTCATCTC 
                 hypomethylation 
                 32 
               
               
                   
                   
                   
                   
                 CCGGCCCTCGAGCCCAGATCCT 
                   
                   
               
               
                   
                   
                   
                   
                 GACGT[CG]TCTGATCCGCCAG 
                   
                   
               
               
                   
                   
                   
                   
                 TCCAGGCTGCCCCGAAGGCGTG 
                   
                   
               
               
                   
                   
                   
                   
                 CGCGGACTGCCGGC 
                   
                   
               
               
                   
               
               
                 CD86_P3_F 
                 CD86 
                 NM_006889.2 
                 29029570 
                 GAACAGCTTCTCTTAAAGAAAG 
                 hypomethylation 
                 33 
               
               
                   
                   
                   
                   
                 TTAGCTGGGTAGGTATACAGTC 
                   
                   
               
               
                   
                   
                   
                   
                 ATTGC[CG]AGGAAGGCTTGCA 
                   
                   
               
               
                   
                   
                   
                   
                 CAGGGTGAAAGCTTTGCTTCTC 
                   
                   
               
               
                   
                   
                   
                   
                 TGCTGCTGTAACAG 
                   
                   
               
               
                   
               
               
                 PADI4_E24_F 
                 PADI4 
                 NM_012387.1 
                 6912575 
                 AGGAACCAGCCCAGGGGCTTCC 
                 hypomethylation 
                 34 
               
               
                   
                   
                   
                   
                 TACAGCCAGAGGGACGAGCTAG 
                   
                   
               
               
                   
                   
                   
                   
                 CCCGA[CG]ATGGCCCAGGGGA 
                   
                   
               
               
                   
                   
                   
                   
                 CATTGATCCGTGTGACCCCAGA 
                   
                   
               
               
                   
                   
                   
                   
                 GCAGCCCACCCATG 
                   
                   
               
               
                   
               
               
                 RHOH_P953_R 
                 RHOH 
                 NM_004310.2 
                 45827772 
                 GCCAACCTCTTTCCCACCTCAG 
                 hypermethylation 
                 35 
               
               
                   
                   
                   
                   
                 GGCCTTTGCACATACTATTTGC 
                   
                   
               
               
                   
                   
                   
                   
                 CTCTA[CG]TGGAATGTTCTTT 
                   
                   
               
               
                   
                   
                   
                   
                 CCTCCTTCTCATCCATTAGAGT 
                   
                   
               
               
                   
                   
                   
                   
                 GGCAGCAGTACTTT 
                   
                   
               
               
                   
               
               
                 FGF1_P357_R 
                 FGF1 
                 NM_033136.1 
                 15055540 
                 CAGGAACACAGAGCCATTGGCC 
                 hypermethylation 
                 36 
               
               
                   
                   
                   
                   
                 AGCCAGGAGGGAGGTAGAGACA 
                   
                   
               
               
                   
                   
                   
                   
                 GAAGA[CG]GTGGCAGCAGCTA 
                   
                   
               
               
                   
                   
                   
                   
                 CCCTGGGTGTTATTTTAACGTG 
                   
                   
               
               
                   
                   
                   
                   
                 GTTTGTCTTGGGGC 
                   
                   
               
               
                   
               
               
                 CSF1R_E26_F 
                 CSF1R 
                 NM_005211.2 
                 27262658 
                 TCCTCTTCCTCTTCTCTCTTCT 
                 hypomethylation 
                 37 
               
               
                   
                   
                   
                   
                 CCACCTTCTCCTCACTTCGTGC 
                   
                   
               
               
                   
                   
                   
                   
                 TCTCA[CG]CTTTTGGACACTC 
                   
                   
               
               
                   
                   
                   
                   
                 TGTCTGCCCTTCTCCTACCTGG 
                   
                   
               
               
                   
                   
                   
                   
                 GGCCTGATCATGAC 
                   
                   
               
               
                   
               
               
                 SPARC_P195_F 
                 SPARC 
                 NM_003118.2 
                 48675809 
                 GGTGGGCTGTCCTGACCAAACG 
                 hypomethylation 
                 38 
               
               
                   
                   
                   
                   
                 TCCCAACCCTGCCTGCCTCATC 
                   
                   
               
               
                   
                   
                   
                   
                 TGTTC[CG]GGGCTGCTGCCTA 
                   
                   
               
               
                   
                   
                   
                   
                 AACCGACTCACAGAGTGCCAGG 
                   
                   
               
               
                   
                   
                   
                   
                 GCTGGACAGGCCTG 
                   
                   
               
               
                   
               
               
                 ITK_P114_F 
                 ITK 
                 NM_005546.3 
                 21614549 
                 TTTTTTACATATGCCTCCTCGT 
                 hypermethylation 
                 39 
               
               
                   
                   
                   
                   
                 TTTGTGAATTTTGAAAGGATGT 
                   
                   
               
               
                   
                   
                   
                   
                 GGTTT[CG]GCCTTTGACATCA 
                   
                   
               
               
                   
                   
                   
                   
                 GAGGAGAAGCTCAGCTATGTTG 
                   
                   
               
               
                   
                   
                   
                   
                 GCTGAACGTTGATA 
                   
                   
               
               
                   
               
               
                 ITK_E166_R 
                 ITK 
                 NM_005546.3 
                 21614549 
                 CAAGAAATCCCAACAAAAGAGA 
                 hypermethylation 
                 40 
               
               
                   
                   
                   
                   
                 AGAACTTCTCCCTCGAACTTTA 
                   
                   
               
               
                   
                   
                   
                   
                 AAGTC[CG]CTTCTTTGTGTTA 
                   
                   
               
               
                   
                   
                   
                   
                 ACCAAAGCCAGCCTGGCATACT 
                   
                   
               
               
                   
                   
                   
                   
                 TTGAAGATCGTCAT 
                   
                   
               
               
                   
               
               
                 LTA_P214_R 
                 LTA 
                 NM_000595.2 
                 6806892 
                 CTCCCAGCCCACGATTCCCCTG 
                 hypermethylation 
                 41 
               
               
                   
                   
                   
                   
                 ACCCGACTCCCTTTCCCAGAAC 
                   
                   
               
               
                   
                   
                   
                   
                 TCAGT[CG]CCTGAACCCCCAG 
                   
                   
               
               
                   
                   
                   
                   
                 CCTGTGGTTCTCTCCTAGGCCT 
                   
                   
               
               
                   
                   
                   
                   
                 CAGCCTTTCCTGCC 
                   
                   
               
               
                   
               
               
                 NOTCH4_E4_F 
                 NOTCH4 
                 NM_004557.3 
                 55770875 
                 TCTGCTCCCACTGCCCCTCTTC 
                 hypomethylation 
                 42 
               
               
                   
                   
                   
                   
                 TTCCTCCTCGGCCTGCTGCAAG 
                   
                   
               
               
                   
                   
                   
                   
                 CCTCA[CG]TCTGAGCTGTTTC 
                   
                   
               
               
                   
                   
                   
                   
                 CTGAGTCACACAATGTCCTGGA 
                   
                   
               
               
                   
                   
                   
                   
                 CACCCTAGTAATGG 
                   
                   
               
               
                   
               
               
                 NOTCH4_P938_F 
                 NOTCH4 
                 NM_004557.3 
                 55770875 
                 GTTGAGGCACTCATGGCTGCTG 
                 hypermethylation 
                 43 
               
               
                   
                   
                   
                   
                 CTGGTGCACCTGAGAGCCTTCC 
                   
                   
               
               
                   
                   
                   
                   
                 CCTAC[CG]GGGAATATACTTC 
                   
                   
               
               
                   
                   
                   
                   
                 ACCAGCACCACTTTCTTCCTTT 
                   
                   
               
               
                   
                   
                   
                   
                 TTTTAGCTTTTTAT 
                   
                   
               
               
                   
               
               
                 RUNX3_E27_R 
                 RUNX3 
                 NM_001031680.1 
                 72534651 
                 ATCATTAGATGGCGGGAAGGGG 
                 hypermethylation 
                 44 
               
               
                   
                   
                   
                   
                 CTTTCGGCAGCCAGGGTGGAGG 
                   
                   
               
               
                   
                   
                   
                   
                 AGCTC[CG]AAGCTGACAGAGC 
                   
                   
               
               
                   
                   
                   
                   
                 AGAGTGGGCCGCCTCCAGTGCC 
                   
                   
               
               
                   
                   
                   
                   
                 ACGGGGAATGAATG 
                   
                   
               
               
                   
               
               
                 GPR116_P850_F 
                 GPR116 
                 NM_015234.3 
                 44771172 
                 CCTCTGCAGCGCTCCCTTTCCC 
                 hypermethylation 
                 45 
               
               
                   
                   
                   
                   
                 TTTCCCTTTCCTGGTTCTCAAG 
                   
                   
               
               
                   
                   
                   
                   
                 GCTCC[CG]AGCTTATGCCTTT 
                   
                   
               
               
                   
                   
                   
                   
                 TCTCCTTCTATGCTCCCATCCT 
                   
                   
               
               
                   
                   
                   
                   
                 CATCATCCTGCAGC 
                   
                   
               
               
                   
               
               
                 RAB32_E314_R 
                 RAB32 
                 NM_006834.2 
                 20127508 
                 TGGTGATCGGCGAGCTTGGCGT 
                 hypomethylation 
                 46 
               
               
                   
                   
                   
                   
                 GGGCAAGACCAGCATCATCAAG 
                   
                   
               
               
                   
                   
                   
                   
                 CGCTA[CG]TCCACCAGCTCTT 
                   
                   
               
               
                   
                   
                   
                   
                 CTCCCAGCACTACCGGGCCACC 
                   
                   
               
               
                   
                   
                   
                   
                 ATCGGGGTGGACTT 
                   
                   
               
               
                   
               
               
                 ESR1_P151_R 
                 ESR1 
                 NM_000125.2 
                 62821793 
                 GGCACATAAGGCAGCACATTAG 
                 hypomethylation 
                 47 
               
               
                   
                   
                   
                   
                 AGAAAGCCGGCCCCTGGATCCG 
                   
                   
               
               
                   
                   
                   
                   
                 TCTTT[CG]CGTTTATTTTAAG 
                   
                   
               
               
                   
                   
                   
                   
                 CCCAGTCTTCCCTGGGCCACCT 
                   
                   
               
               
                   
                   
                   
                   
                 TTAGCAGATCCTCG 
                   
                   
               
               
                   
               
               
                 IL6_P213_R 
                 IL6 
                 NM_000600.1 
                 10834983 
                 AAGAAAGTAAAGGAAGAGTGGT 
                 hypomethylation 
                 48 
               
               
                   
                   
                   
                   
                 TCTGCTTCTTAGCGCTAGCCTC 
                   
                   
               
               
                   
                   
                   
                   
                 AATGA[CG]ACCTAAGCTGCAC 
                   
                   
               
               
                   
                   
                   
                   
                 TTTTCCCCCTAGTTGTGTCTTG 
                   
                   
               
               
                   
                   
                   
                   
                 CCATGCTAAAGGAC 
                   
                   
               
               
                   
               
               
                 CLDN4_P1120_R 
                 CLDN4 
                 NM_001305.3 
                 34335232 
                 CTCCCCAGCCCAGTCTCTGGTC 
                 hypermethylation 
                 49 
               
               
                   
                   
                   
                   
                 AAACTGGATTCCTGGCTGTTCC 
                   
                   
               
               
                   
                   
                   
                   
                 CAGAA[CG]AGCTGCCTTTCCC 
                   
                   
               
               
                   
                   
                   
                   
                 CACCTTGCCACCTCTGCCCTTG 
                   
                   
               
               
                   
                   
                   
                   
                 TTCTCTCTGCCTGA 
                   
                   
               
               
                   
               
               
                 HGF_E102_R 
                 HGF 
                 NM_001010933.1 
                 58533164 
                 GGGCTGGCGGATCCCTCTGGAG 
                 hypomethylation 
                 50 
               
               
                   
                   
                   
                   
                 GAGATGCCTGGGTGAAAGAATC 
                   
                   
               
               
                   
                   
                   
                   
                 CTGTT[CG]GAGTCAGTGCCTA 
                   
                   
               
               
                   
                   
                   
                   
                 AAAGAGCCAGTCGGCTCTGAGC 
                   
                   
               
               
                   
                   
                   
                   
                 TGCTTTTTATTGCG 
                   
                   
               
               
                   
               
               
                 TFPI2_P152_R 
                 TFPI2 
                 NM_006528.2 
                 31543803 
                 ACCCCGCCGCCCCCGCGCTGCA 
                 hypomethylation 
                 51 
               
               
                   
                   
                   
                   
                 AACTGTGTAAGAGGGAGAGGAA 
                   
                   
               
               
                   
                   
                   
                   
                 TTCCC[CG]CCAAGTTGAAAAG 
                   
                   
               
               
                   
                   
                   
                   
                 TTGAACCTGCCTCCCAAACTTT 
                   
                   
               
               
                   
                   
                   
                   
                 CTCCTGTAGTCCAG 
                   
                   
               
               
                   
               
               
                 TRIP6_P1274_R 
                 TRIP6 
                 NM_003302.1 
                 23308730 
                 TCCTGCTGCAGATGGCAACCAT 
                 hypomethylation 
                 52 
               
               
                   
                   
                   
                   
                 CTTGGGCATGGTGCCCGCTTGG 
                   
                   
               
               
                   
                   
                   
                   
                 CATAG[CG]CCCGGCTCCGGAT 
                   
                   
               
               
                   
                   
                   
                   
                 CTTCCTGTGCCTGGGGCCTCGG 
                   
                   
               
               
                   
                   
                   
                   
                 GAGGCGCCTGGGGC 
                   
                   
               
               
                   
               
               
                 RUNX3_P247_F 
                 RUNX3 
                 NM_001031680.1 
                 72534651 
                 CACAGGATGCGAGAAGCCTGCT 
                 hypermethylation 
                 53 
               
               
                   
                   
                   
                   
                 CGCGGCCTTGGCTCATTGGCTG 
                   
                   
               
               
                   
                   
                   
                   
                 GGCCG[CG]GTCACCTGGGCCG 
                   
                   
               
               
                   
                   
                   
                   
                 TGATGTCACGGCCTTTTAGAAG 
                   
                   
               
               
                   
                   
                   
                   
                 ATCTTGTGGCTGCC 
                   
                   
               
               
                   
               
               
                 TRIP6_P1090_F 
                 TRIP6 
                 NM_003302.1 
                 23308730 
                 GGCTGGGGAACCCGAGGCGGAG 
                 hypomethylation 
                 54 
               
               
                   
                   
                   
                   
                 GAGGAAGGGGACTTTGTGAACA 
                   
                   
               
               
                   
                   
                   
                   
                 GTGGG[CG]GGGAGACGCAGAG 
                   
                   
               
               
                   
                   
                   
                   
                 GCAGAGGCCCTGGCACGCAGCG 
                   
                   
               
               
                   
                   
                   
                   
                 CCAACGCCCTGGTT 
                   
                   
               
               
                   
               
               
                 CPA4_E20_F 
                 CPA4 
                 NM_016352.2 
                 61743915 
                 AGACTCTTTATAAATACAGCTT 
                 hypermethylation 
                 55 
               
               
                   
                   
                   
                   
                 GACTCAGCCACTGTATGACTGA 
                   
                   
               
               
                   
                   
                   
                   
                 CTCCC[CG]GGGACATGAGGTG 
                   
                   
               
               
                   
                   
                   
                   
                 GATACTGTTCATTGGGGCCCTT 
                   
                   
               
               
                   
                   
                   
                   
                 ATTGGGTCCAGCAT 
                   
                   
               
               
                   
               
               
                 SYK_P584_F 
                 SYK 
                 NM_003177.3 
                 34147655 
                 CCATTCTTAGGGCTATAGGTTT 
                 hypomethylation 
                 56 
               
               
                   
                   
                   
                   
                 AATTTATTTGGTTGTGGACGTC 
                   
                   
               
               
                   
                   
                   
                   
                 AGAGC[CG]TCATGGTAAGAAG 
                   
                   
               
               
                   
                   
                   
                   
                 GAAGCAAAGCCTTTTGTAATAA 
                   
                   
               
               
                   
                   
                   
                   
                 TTAAAGCCTTCAGA 
                   
                   
               
               
                   
               
               
                 LCN2_P141_R 
                 LCN2 
                 NM_005564.2 
                 38455401 
                 GTTGTCCCTGCCAGAGGTGCAG 
                 hypomethylation 
                 57 
               
               
                   
                   
                   
                   
                 CACTCCGGGAATGTCCCTCACT 
                   
                   
               
               
                   
                   
                   
                   
                 CTCCC[CG]TCCCTCTGTCTTG 
                   
                   
               
               
                   
                   
                   
                   
                 CCCAATCCTGACCAGGTGCAGA 
                   
                   
               
               
                   
                   
                   
                   
                 AATCTTGCCAAGTG 
                   
                   
               
               
                   
               
               
                 LCN2_P86_R 
                 LCN2 
                 NM_005564.2 
                 38455401 
                 TCTGTCTTGCCCAATCCTGACC 
                 hypomethylation 
                 58 
               
               
                   
                   
                   
                   
                 AGGTGCAGAAATCTTGCCAAGT 
                   
                   
               
               
                   
                   
                   
                   
                 GTTTC[CG]CAGGAGTTGCTGG 
                   
                   
               
               
                   
                   
                   
                   
                 CAATTGCCTCACATTCCTGGCC 
                   
                   
               
               
                   
                   
                   
                   
                 TTGGCAAAGAATGA 
                   
                   
               
               
                   
               
               
                 SLC22A18_P472__R 
                 SLC22A18 
                 NM_002555.3 
                 34734074 
                 TGCCCAGCGCTCCCAGGGTCAC 
                 hypomethylation 
                 59 
               
               
                   
                   
                   
                   
                 CCCTCTCTCTAGACTCACTTTC 
                   
                   
               
               
                   
                   
                   
                   
                 TGCCC[CG]TCACCCCACTGTA 
                   
                   
               
               
                   
                   
                   
                   
                 CACCCTTGGTCCCAGCCCCTTC 
                   
                   
               
               
                   
                   
                   
                   
                 CAGTGGCTCAGCTT 
                   
                   
               
               
                   
               
               
                 SLC22A18P216_R 
                 SLC22A18 
                 NM_002555.3 
                 34734074 
                 AGATGAGCCAAAGCCCTTCCTT 
                 hypomethylation 
                 60 
               
               
                   
                   
                   
                   
                 CCTCCAGTCAGCCTGGATCCTC 
                   
                   
               
               
                   
                   
                   
                   
                 TCATC[CG]GCAGAACTGTCGC 
                   
                   
               
               
                   
                   
                   
                   
                 CTTGCTTCTCTGAAGCGGTGAA 
                   
                   
               
               
                   
                   
                   
                   
                 TGCCCTGGGGCTGG 
                   
                   
               
               
                   
               
               
                 RUNX3_P393_R 
                 RUNX3 
                 NM_001031680.1 
                 72534651 
                 GAGAAATAGAAAAGTGATGGCT 
                 hypermethylation 
                 61 
               
               
                   
                   
                   
                   
                 TTTATTTGTGAGGCTGGCCTCA 
                   
                   
               
               
                   
                   
                   
                   
                 GCACG[CG]GCCCAAGAAACAG 
                   
                   
               
               
                   
                   
                   
                   
                 AACTGAAAGCGGTTGCAGTGGG 
                   
                   
               
               
                   
                   
                   
                   
                 CGTGGCCAGGAGGG 
                   
                   
               
               
                   
               
               
                 LMO2_E148_F 
                 LMO2 
                 NM_005574.2 
                 6633806 
                 TTGGTGGCCTGGTTGTCTATCT 
                 hypomethylation 
                 62 
               
               
                   
                   
                   
                   
                 GATAGGGCGGAGCCTTCACCCT 
                   
                   
               
               
                   
                   
                   
                   
                 TGCAG[CG]AGCTCTCTCACAC 
                   
                   
               
               
                   
                   
                   
                   
                 CAGATGTGCTCTGCGTGGAATC 
                   
                   
               
               
                   
                   
                   
                   
                 CTAGGCCATCAGGG 
                   
                   
               
               
                   
               
               
                 LMO2_P794_R 
                 LMO2 
                 NM_005574.2 
                 6633806 
                 CAGCTACCTCCCCCGCATGCAT 
                 hypomethylation 
                 63 
               
               
                   
                   
                   
                   
                 GTCTGTCTGCTGGGCAAGGCCC 
                   
                   
               
               
                   
                   
                   
                   
                 AATTC[CG]AGGTGACAGCTCA 
                   
                   
               
               
                   
                   
                   
                   
                 CCGGGCCTCACCCACAAGTCTC 
                   
                   
               
               
                   
                   
                   
                   
                 TTCCAAGCATTAGC 
                   
                   
               
               
                   
               
               
                 CD82_P557_R 
                 CD82 
                 NM_002231.3 
                 67782352 
                 GATTCAATCAATGGTAGTCAGT 
                 hypomethylation 
                 64 
               
               
                   
                   
                   
                   
                 ATTTTCAAAAAGTTCCTGGGCC 
                   
                   
               
               
                   
                   
                   
                   
                 CAGGC[CG]CCTCCTGATAGAG 
                   
                   
               
               
                   
                   
                   
                   
                 GCCCCGACTTAGGACACAAACC 
                   
                   
               
               
                   
                   
                   
                   
                 GCTCCCACGCCGTT 
                   
                   
               
               
                   
               
               
                 SPI1_E205_F 
                 SPI1 
                 NM_003120.1 
                 4507174 
                 GAGTCCCGGTACTCACAGGGGG 
                 hypomethylation 
                 65 
               
               
                   
                   
                   
                   
                 GACGAGGGGAAACCCTTCCATT 
                   
                   
               
               
                   
                   
                   
                   
                 TTGCA[CG]CCTGTAACATCCA 
                   
                   
               
               
                   
                   
                   
                   
                 GCCGGGCTCCGAGTCGGTCAGA 
                   
                   
               
               
                   
                   
                   
                   
                 TCCCCTGCCTCGGT 
                   
                   
               
               
                   
               
               
                 SPI1_P48_F 
                 SPI1 
                 NM_003120.1 
                 4507174 
                 TTATCGAAGGGCCTGCCGCTGA 
                 hypomethylation 
                 66 
               
               
                   
                   
                   
                   
                 GGAGATAGTCCCCTTGGGGTGC 
                   
                   
               
               
                   
                   
                   
                   
                 ATCAC[CG]CCCCAACCCGTTT 
                   
                   
               
               
                   
                   
                   
                   
                 GCATAAATCTCTTGCGCTACAT 
                   
                   
               
               
                   
                   
                   
                   
                 ACAGGAAGTCTCTG 
                   
                   
               
               
                   
               
               
                 KCNK4_E3_F 
                 KCNK4 
                 NM_016611.2 
                 15718764 
                 CCGATCCGGTAATGGGCCTGGG 
                 hypomethylation 
                 67 
               
               
                   
                   
                   
                   
                 AGATGCCAGATTAGCGTGGTGC 
                   
                   
               
               
                   
                   
                   
                   
                 CTGTC[CG]GAGAGACGGGCCA 
                   
                   
               
               
                   
                   
                   
                   
                 GCTGATGCCCAGGTCGGGGCCC 
                   
                   
               
               
                   
                   
                   
                   
                 TGCCGCTGGCCACA 
                   
                   
               
               
                   
               
               
                 MMP8_E89_R 
                 MMP8 
                 NM_002424.1 
                 4505220 
                 CAGGAAAGGCCTTGGAAATCTG 
                 hypomethylation 
                 68 
               
               
                   
                   
                   
                   
                 CACATGGAGTAAGAGCAGAAAT 
                   
                   
               
               
                   
                   
                   
                   
                 GGAAG[CG]TCTTCAGGGAGAA 
                   
                   
               
               
                   
                   
                   
                   
                 CATGATCTTCTCTTCAAACTCT 
                   
                   
               
               
                   
                   
                   
                   
                 ACCCCTCCTGGCTT 
                   
                   
               
               
                   
               
               
                 CD9_P585_R 
                 CD9 
                 NM_001769.2 
                 21237762 
                 TTTGCTAATTACTTCCAAAAGC 
                 hypomethylation 
                 69 
               
               
                   
                   
                   
                   
                 CTCCCATCTGTCATCCCACCCA 
                   
                   
               
               
                   
                   
                   
                   
                 GACTG[CG]CGCTTCTAATTCC 
                   
                   
               
               
                   
                   
                   
                   
                 TCCTACCCCACATGCTGTGCCC 
                   
                   
               
               
                   
                   
                   
                   
                 AATGAAAAGTATGG 
                   
                   
               
               
                   
               
               
                 CD9_P504_F 
                 CD9 
                 NM_001769.2 
                 21237762 
                 TGCCCAATGAAAAGTATGGTCA 
                 hypomethylation 
                 70 
               
               
                   
                   
                   
                   
                 GCGAGCGAAGGTTTGCAAGGAG 
                   
                   
               
               
                   
                   
                   
                   
                 ACAGA[CG]AGGGCGAAATTAA 
                   
                   
               
               
                   
                   
                   
                   
                 GCCAGGCGGCTTCCCTTTAAAT 
                   
                   
               
               
                   
                   
                   
                   
                 CCTCGCAAAGCAGA 
                   
                   
               
               
                   
               
               
                 LCK_E28_F 
                 LCK 
                 NM_005356.2 
                 20428651 
                 GCAGCCAGGTTAGGCCAGGAGG 
                 hypermethylation 
                 71 
               
               
                   
                   
                   
                   
                 ACCATGTGAATGGGGCCAGAGG 
                   
                   
               
               
                   
                   
                   
                   
                 GCTCC[CG]GGCTGGGCAGGTA 
                   
                   
               
               
                   
                   
                   
                   
                 AGGAGCGCTGGTATTGGGGGCG 
                   
                   
               
               
                   
                   
                   
                   
                 CAGGCGCCGGGGTG 
                   
                   
               
               
                   
               
               
                 TNFRSF1A_P678__F 
                 TNFRSF1A 
                 NM_001065.2 
                 23312372 
                 GTCCCCCCACCCTGCCCCACTG 
                 hypomethylation 
                 72 
               
               
                   
                   
                   
                   
                 TTGATCCTGGCTCTGCCACCAA 
                   
                   
               
               
                   
                   
                   
                   
                 TCATG[CG]ACATCAGGCAACT 
                   
                   
               
               
                   
                   
                   
                   
                 CCTCTCCTAAGCCTCTGTTGGT 
                   
                   
               
               
                   
                   
                   
                   
                 TCCTTGTTTATTAA 
                   
                   
               
               
                   
               
               
                 PTPN6_P282_R 
                 PTPN6 
                 NM_080548.2 
                 34328901 
                 AGGAACTGGGCTGTTAGGGATT 
                 hypomethylation 
                 73 
               
               
                   
                   
                   
                   
                 TTCCTTAGGCCCTTTGGTTTCC 
                   
                   
               
               
                   
                   
                   
                   
                 GCCTA[CG]GAGAGGTTTCCCC 
                   
                   
               
               
                   
                   
                   
                   
                 CATTGGTTGCTCTTCCTCAGCC 
                   
                   
               
               
                   
                   
                   
                   
                 AGGGTTACTTCCTG 
                   
                   
               
               
                   
               
               
                 TM7SF3_P1068_R 
                 TM7SF3 
                 NM_016551.1 
                 7706574 
                 ACCACTGCAACTGGGTCTTGCA 
                 hypomethylation 
                 74 
               
               
                   
                   
                   
                   
                 GTGGGGAAGAGGGACTGGGCTC 
                   
                   
               
               
                   
                   
                   
                   
                 AACTC[CG]AATACAGCGTGGG 
                   
                   
               
               
                   
                   
                   
                   
                 CAAGAGGGAATTTATAGCCAAC 
                   
                   
               
               
                   
                   
                   
                   
                 CAGCAGTATGGAGT 
                   
                   
               
               
                   
               
               
                 KRT1_P798_R 
                 KRT1 
                 NM_006121.2 
                 17318568 
                 GGATAGCATGCAAACGCCCTTG 
                 hypermethylation 
                 75 
               
               
                   
                   
                   
                   
                 AGTGAAAAAGCCCACAGAGCAG 
                   
                   
               
               
                   
                   
                   
                   
                 TGAGA[CG]AGTAAATAGAAGC 
                   
                   
               
               
                   
                   
                   
                   
                 TCTAGGACATTTTGTAAAGCAC 
                   
                   
               
               
                   
                   
                   
                   
                 AGGGGTGGAGGTGA 
                   
                   
               
               
                   
               
               
                 IFNG E293_F 
                 IFNG 
                 NM_000619.2 
                 56786137 
                 AATGACTGCCTACAAGAGATGA 
                 hypermethylation 
                 76 
               
               
                   
                   
                   
                   
                 CAGCCTATCAGAGATGCTACAG 
                   
                   
               
               
                   
                   
                   
                   
                 CAAGT[CG]ATATTCAGTCATT 
                   
                   
               
               
                   
                   
                   
                   
                 TTCAACCACAAACAAGTACTAT 
                   
                   
               
               
                   
                   
                   
                   
                 TAAAAAGTCATACT 
                   
                   
               
               
                   
               
               
                 IFNG_P459_R 
                 IFNG 
                 NM_000619.2 
                 56786137 
                 AGCCTTTTAAAATTTTTCTTGC 
                 hypermethylation 
                 77 
               
               
                   
                   
                   
                   
                 AAATGACCAGAAAGCAAGGAAA 
                   
                   
               
               
                   
                   
                   
                   
                 GAATG[CG]GTTAAAAGAACAA 
                   
                   
               
               
                   
                   
                   
                   
                 TTTGGTGAGGAAGTCCTTCATC 
                   
                   
               
               
                   
                   
                   
                   
                 AGAGTTGGTTAGTA 
                   
                   
               
               
                   
               
               
                 MMP14_P13_F 
                 MMP14 
                 NM_004995.2 
                 13027797 
                 CGGGGACGGAGGAGAGGCTGTG 
                 hypomethylation 
                 78 
               
               
                   
                   
                   
                   
                 GGAGAAGGGAGGGACCAGAGGA 
                   
                   
               
               
                   
                   
                   
                   
                 GAGAG[CG]AGAGAGGGAACCA 
                   
                   
               
               
                   
                   
                   
                   
                 GACCCCAGTTCGCCGACTAAGC 
                   
                   
               
               
                   
                   
                   
                   
                 AGAAGAAAGATCAA 
                   
                   
               
               
                   
               
               
                 BCL2L2_P280_F 
                 BCL2L2 
                 NM_004050.2 
                 14574571 
                 CCAGGCACACAGTTCAGGGCTG 
                 hypomethylation 
                 79 
               
               
                   
                   
                   
                   
                 GAAAAGTTCAACAAGTGCATGG 
                   
                   
               
               
                   
                   
                   
                   
                 AACAT[CG]GAAACCTCCTGAA 
                   
                   
               
               
                   
                   
                   
                   
                 AATGCTAAATTTGCCCCGAGAT 
                   
                   
               
               
                   
                   
                   
                   
                 GTCCCGAAGTCCGG 
                   
                   
               
               
                   
               
               
                 CRIP1_P874_R 
                 CRIP1 
                 NM_001311.3 
                 39725694 
                 GCCTGGCACCGGGACCATCCTC 
                 hypomethylation 
                 80 
               
               
                   
                   
                   
                   
                 CGCCTCAACTTTGCAGCGTACT 
                   
                   
               
               
                   
                   
                   
                   
                 TGGAC[CG]CTCTGGCCGCCCT 
                   
                   
               
               
                   
                   
                   
                   
                 GGGCGCTACCCGCAGAGATAAG 
                   
                   
               
               
                   
                   
                   
                   
                 GGCCCCTCCCTGCG 
                   
                   
               
               
                   
               
               
                 APBA2_P227_F 
                 APBA2 
                 NM_005503.2 
                 22035549 
                 CCTTTGGAAATAAACACGAAGG 
                 hypermethylation 
                 81 
               
               
                   
                   
                   
                   
                 TTCACTTGAAGACTTGGGGGAG 
                   
                   
               
               
                   
                   
                   
                   
                 AATCA[CG]GTCAACTTGTGAC 
                   
                   
               
               
                   
                   
                   
                   
                 GCTTGGTTTTTCAGATATTCAG 
                   
                   
               
               
                   
                   
                   
                   
                 CTGCTCTGGAGAGC 
                   
                   
               
               
                   
               
               
                 CSF3R_P8_F 
                 CSF3R 
                 NM_172313.1 
                 27437044 
                 AGAAGTTCCTGAAACCAGCTGC 
                 hypomethylation 
                 82 
               
               
                   
                   
                   
                   
                 AGTCCAGCTTCTCTCCCCGAGC 
                   
                   
               
               
                   
                   
                   
                   
                 TCTGT[CG]TTAATGGCTCAGC 
                   
                   
               
               
                   
                   
                   
                   
                 CTCTGACAGGCCCGGGGGCTGG 
                   
                   
               
               
                   
                   
                   
                   
                 GGATTGCAACACCT 
                   
                   
               
               
                   
               
               
                 CARD15_P302_R 
                 CARD15 
                 NM_022162.1 
                 11545911 
                 TGGTGATGTAGCTGCTGGGAGG 
                 hypomethylation 
                 83 
               
               
                   
                   
                   
                   
                 ACAGAGCTCCGAGTCACGTGGC 
                   
                   
               
               
                   
                   
                   
                   
                 TTGGG[CG]GGCCTCCCCTTCC 
                   
                   
               
               
                   
                   
                   
                   
                 TGGTGTCCACAGAAGCCCAACG 
                   
                   
               
               
                   
                   
                   
                   
                 TCACTAGCTGGGGT 
                   
                   
               
               
                   
               
               
                 ALOX12_E85_R 
                 ALOX12 
                 NM_000697.1 
                 4502050 
                 GGCCGCTACCGCATCCGCGTGG 
                 hypomethylation 
                 84 
               
               
                   
                   
                   
                   
                 CCACCGGGGCCTGGCTCTTCTC 
                   
                   
               
               
                   
                   
                   
                   
                 CGGGT[CG]TACAACCGCGTGC 
                   
                   
               
               
                   
                   
                   
                   
                 AGCTTTGGCTGGTCGGGACGCG 
                   
                   
               
               
                   
                   
                   
                   
                 CGGGGAGGCGGAGC 
                   
                   
               
               
                   
               
               
                 MFAP4_P197_F 
                 MFAP4 
                 NM_002404.1 
                 23111004 
                 GGGAGGTGGGGCTGGAGCCAGG 
                 hypomethylation 
                 85 
               
               
                   
                   
                   
                   
                 GGACCACCTGTGTCTCATTAGT 
                   
                   
               
               
                   
                   
                   
                   
                 CCTGT[CG]GGCAAAGTACTGC 
                   
                   
               
               
                   
                   
                   
                   
                 AGACGTTAACTCCCTGCTGGCT 
                   
                   
               
               
                   
                   
                   
                   
                 CCAACTGTTCCCTG 
                   
                   
               
               
                   
               
               
                 GRB7_P160_R 
                 GRB7 
                 NM_001030002.1 
                 71979666 
                 CGGGACTCTTGATCTTCGCTCG 
                 hypomethylation 
                 86 
               
               
                   
                   
                   
                   
                 TGGTACTGTCTGTTCGGCTGTC 
                   
                   
               
               
                   
                   
                   
                   
                 TTCCC[CG]CCTCTCCCCAGGC 
                   
                   
               
               
                   
                   
                   
                   
                 ACCTGCATCCTCCCTTGGCACC 
                   
                   
               
               
                   
                   
                   
                   
                 TGCTGCCAGGCTAG 
                   
                   
               
               
                   
               
               
                 GRB7_E71_R 
                 GRB7 
                 NM_001030002.1 
                 71979666 
                 ATCTGGACACACAGGGCTCCCC 
                 hypomethylation 
                 87 
               
               
                   
                   
                   
                   
                 CCCGCCTCTGACTTCTCTGTCC 
                   
                   
               
               
                   
                   
                   
                   
                 GAAGT[CG]GGACACCCTCCTA 
                   
                   
               
               
                   
                   
                   
                   
                 CCACCTGTAGAGAAGCGGGAGT 
                   
                   
               
               
                   
                   
                   
                   
                 GGATCTGAAATAAA 
                   
                   
               
               
                   
               
               
                 CSF3_E242_R 
                 CSF3 
                 NM_172220.1 
                 27437050 
                 TGTCCCCGAGAGGGCCTCAGGT 
                 hypomethylation 
                 88 
               
               
                   
                   
                   
                   
                 GGTAGGGAACAGCATGTCTCCT 
                   
                   
               
               
                   
                   
                   
                   
                 GAGCC[CG]CTCTGTCCCCAGC 
                   
                   
               
               
                   
                   
                   
                   
                 CCTGCAGCTGCTGCTGTGGCAC 
                   
                   
               
               
                   
                   
                   
                   
                 AGTGCACTCTGGAC 
                   
                   
               
               
                   
               
               
                 RARA_P1076_R 
                 RARA 
                 NM_000964.2 
                 75812906 
                 GTCTTCTCCCCTTCTAGGGAGA 
                 hypomethylation 
                 89 
               
               
                   
                   
                   
                   
                 GGCCATGCCCTCTCCCCTCAAG 
                   
                   
               
               
                   
                   
                   
                   
                 TCTGT[CG]CTGACTTCCTCTG 
                   
                   
               
               
                   
                   
                   
                   
                 GCCCTTCCCCTCATGACGTTTT 
                   
                   
               
               
                   
                   
                   
                   
                 CCCTGCTCTGCTGC 
                   
                   
               
               
                   
               
               
                 STAT5A _P704_R 
                 STAT5A 
                 NM_003152.2 
                 21618341 
                 ACCCAAATGTGGCAATGGGTTT 
                 hypomethylation 
                 90 
               
               
                   
                   
                   
                   
                 GTATCCAGCCACCGACAGGCTG 
                   
                   
               
               
                   
                   
                   
                   
                 CATGA[CG]GTGGCAAAGTCAC 
                   
                   
               
               
                   
                   
                   
                   
                 TTCCCCTCTCTGGCCTTTGTTT 
                   
                   
               
               
                   
                   
                   
                   
                 TTCCACTTGTAAAA 
                   
                   
               
               
                   
               
               
                 CSF3R_P472_F 
                 CSF3R 
                 NM_172313.1 
                 27437044 
                 GGTTCCAGGGAATTGTGTAACC 
                 hypomethylation 
                 91 
               
               
                   
                   
                   
                   
                 CAATACTCACTGCTCCCCTCTT 
                   
                   
               
               
                   
                   
                   
                   
                 CATTA[CG]TATTCTGTGCATT 
                   
                   
               
               
                   
                   
                   
                   
                 GCCCATAGACCAGGCAGATGGA 
                   
                   
               
               
                   
                   
                   
                   
                 GAAACAGGAATTCT 
                   
                   
               
               
                   
               
               
                 PECAM1__E32_R 
                 PECAM1 
                 NM_000442.2 
                 21314616 
                 AAATTGCTCTGGTCACTTCTCC 
                 hypomethylation 
                 92 
               
               
                   
                   
                   
                   
                 CGGCGCCTGCAGAGAGACCGGC 
                   
                   
               
               
                   
                   
                   
                   
                 TGTGG[CG]CTGGTCAGGTAAT 
                   
                   
               
               
                   
                   
                   
                   
                 GGCAGCCATGGCTGGAAACCGG 
                   
                   
               
               
                   
                   
                   
                   
                 GAACAATGGGGCCT 
                   
                   
               
               
                   
               
               
                 PECAM1_P135_F 
                 PECAM1 
                 NM_000442.2 
                 21314616 
                 GTTTAGTTTCTTTAGGGAAAAA 
                 hypomethylation 
                 93 
               
               
                   
                   
                   
                   
                 ACAAGGCACAAGTGACATTTGC 
                   
                   
               
               
                   
                   
                   
                   
                 CTTGG[CG]TTCTTGACCCTCC 
                   
                   
               
               
                   
                   
                   
                   
                 CTCTGTCTCGCCTGGGTTTGGG 
                   
                   
               
               
                   
                   
                   
                   
                 GGCCCTTCTCATGG 
                   
                   
               
               
                   
               
               
                 SEPT9_P374_F 
                 SEPT9. 
                 NM_006640.2 
                 19923366 
                 TGGGGTACAGGGTGAAGAAGGG 
                 hypomethylation 
                 94 
               
               
                   
                   
                   
                   
                 CTGGGGCCAGCCCAGGACAGAG 
                   
                   
               
               
                   
                   
                   
                   
                 GAAGG[CG]AGGCAGGCACGCA 
                   
                   
               
               
                   
                   
                   
                   
                 GGAACTGGGCTTTTTAAACCCT 
                   
                   
               
               
                   
                   
                   
                   
                 TAAGCCCAAGGAAA 
                   
                   
               
               
                   
               
               
                 MATK_P190_R 
                 MATK 
                 NM_139355.1 
                 21450845 
                 GGGTGGGAGGCTTCCGAGAGCC 
                 hypomethylation 
                 95 
               
               
                   
                   
                   
                   
                 GCCTCTCCCGGGGCATAAGGAA 
                   
                   
               
               
                   
                   
                   
                   
                 GGAAG[CG]GGGCTGCAGGTAC 
                   
                   
               
               
                   
                   
                   
                   
                 CGCCTGGGGTTCACAGCAGGGG 
                   
                   
               
               
                   
                   
                   
                   
                 ACGAGGTGCCTCCC 
                   
                   
               
               
                   
               
               
                 EMR3_E61_F 
                 EMR3 
                 NM_152939.1 
                 23397638 
                 AGCTGACTCATGAAATTGCTAT 
                 hypomethylation 
                 96 
               
               
                   
                   
                   
                   
                 CAGAAAAGCAAACTGCTTCCCC 
                   
                   
               
               
                   
                   
                   
                   
                 TCTTT[CG]CCATCAGACTCAT 
                   
                   
               
               
                   
                   
                   
                   
                 GGTTCTGCTTTTCGTTTATTTG 
                   
                   
               
               
                   
                   
                   
                   
                 CTGTACCTTTTCTG 
                   
                   
               
               
                   
               
            
           
         
       
     
     Any appropriate method can be used to obtain a blood sample that can be processed to obtain nucleic acid for the assessment of the human&#39;s CpG methylation site profile. For example, leukocyte nucleic acid can be obtained and assessed as described herein to determine whether any one or more of the methylation CpG sites listed in Table 1 or 5 have an altered level of methylation as compared to controls (e.g., healthy humans known to not have pancreatic cancer). In some cases, combinations of methylation CpG sites can be assessed as described herein. Examples of such combinations include, without limitation, (a) IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817; (b) LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817; (c) IL10_P348, ZAP70_P220, AIM2_P624, and TAL1_P817; (d) IL10_P348, LCN2_P86, AIM2_P624, and TAL1_P817; (e) IL10_P348, LCN2_P86, ZAP70_P220, and TAL1_P817; (f) IL10_P348, LCN2_P86, ZAP70_P220, and AIM2_P624; (g) IL10_P348, LCN2_P86, and ZAP70_P220; (h) IL10_P348, LCN2_P86, and AIM2_P624; (i) IL10_P348, LCN2_P86, and TAL1_P817; (j) IL10_P348, ZAP70_P220, and AIM2_P624; (k) IL10_P348, ZAP70_P220, and TAL1_P817; (l) IL10_P348, AIM2_P624, and TAL1_P817; (m) LCN2_P86, ZAP70_P220, and AIM2_P624; (n) LCN2_P86, ZAP70_P220, and TAL1_P817; (o) LCN2_P86, AIM2_P624, and TAL1_P817; (p) ZAP70_P220, AIM2_P624, and TAL1_P817; (q) IL10_P348 and LCN2_P86; (r) IL10_P348 and ZAP70_P220; (s) IL10_P348 and AIM2_P624; (t) IL10_P348 and TAL1_P817; (u) LCN2_P86 and ZAP70_P220; (v) LCN2_P86 and AIM2_P624; (w) LCN2_P86 and TAL1_P817; (x) ZAP70_P220 and AIM2_P624; (y) ZAP70_P220 and TAL1_P817; and (z) AIM2_P624 and TAL1_P817. 
     Any appropriate method can be used to assess a methylation CpG site for methylation level change (e.g., the presence or absence of a methyl group). For example, methylation assays available commercially (e.g., from Illumina) can be used to determine the methylation state of methylation CpG sites. 
     Once a human is determined to having altered levels of methylation of methylation CpG sites that are indicative of pancreatic cancer, then the human can be classified as having pancreatic cancer or can be evaluated further to confirm a diagnosis of pancreatic cancer. Humans identified as having pancreatic cancer as described herein can be treated with any appropriate pancreatic cancer treatment including, without limitation, surgery, radiation, and chemotherapy. 
     The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims. 
     EXAMPLES 
     Example 1  
     Leukocyte DNA Methylation Signature Differentiates Pancreatic Cancer Patients from Healthy Controls 
     Study Population 
     PaC index cases were adult patients with a histologically confirmed primary adenocarcinoma of the pancreas seen at Mayo Clinic. Eligible Mayo pancreatic adenocarcinoma cases were identified through an ultra-rapid patient identification system and recruited into a prospective research registry. Study coordinators identified potential patients from the electronic patient scheduling system and daily pathology reports. All eligible patients were contacted either in the clinic at the time of their appointment, or later by mail or phone if clinic contact was not possible. If contacted at the clinic, a study coordinator obtained informed consent, arranged a venipuncture for 40 mL of blood prior to start of treatment (whenever possible), and asked the participant to complete the study questionnaire. If mail contact was required (approximately 28% of the cases were approached by mail), the study coordinator mailed an invitation letter to the patient&#39;s home address. A follow-up telephone call was made if the sample or forms were not received after one month. About 74% of all eligible patients were enrolled into the registry. From the registry, 132 never-smoker patients in phase I and 240 patients in phase II were selected with equal representation of sex, smoking status (smoker/nonsmoker) and stage of PaC (resectable, locally advanced and metastatic). 
     The healthy Caucasian controls were selected from a Mayo Clinic—based research registry of primary care control patients having routine check-up visits (general medical exam). Controls were frequency-matched to cases on age (±5 years), sex, and state/region of residence distribution of the cases. Controls had no previous diagnosis of cancer (except non-melanoma skin cancer) at the time of enrollment. Prior to their appointment, potential controls were mailed an information brochure describing the study and a letter of invitation. On the day of the appointment, a study assistant approached the subject, confirmed eligibility criteria, and obtained informed consent. Each participant completed study questionnaires (which included a self-report of height, weight, and diabetes status) and provided 30 mL of research blood sample. About 70% of all approached controls participated in this study. From this registry, 60 never smoker controls for phase I and 240 controls (half are never smokers) for phase II were selected. 
     DNA Modification by Sodium Bisulfite 
     DNA was extracted from 5 mL of whole blood utilizing an AutoGen FlexStar (AutoGen, Inc., Mass.), and the genomic DNA specimens were modified using the EZ DNA Methylation kit from Zymo Research Corporation (Orange, Calif.) that combined bisulfite conversion and DNA cleaning. The kit is based on the three-step reaction that takes place between cytosine and sodium bisulfite where cytosine is converted into uracil. 1 μg of genomic DNA from peripheral blood DNA was used for the modification per manufacturer recommendation. Treated DNA specimens were stored at −20° C. and were assayed within two weeks. 
     DNA Methylation Profiling Analysis 
     The Illumina (San Diego, Calif.) GoldenGate methylation Beadchip (cancer panel) and Illumina custom VeraCode methylation assay were used for phase I and phase II, respectively, following the manufacturer&#39;s procedure. The arrays were imaged using a BeadArray Reader scanner (Illumina, Inc.). The proportion methylated (β-value) at each CpG site was calculated using BeadStudio Software (Illumina, Inc.) after subtracting background intensity, which was computed from negative controls, from each analytical data point. The β-value represented relative ratio of fluorescent signals between the M (methylated) allele and M+U (unmethylated) alleles. This value ranges continuously from 0 (unmethylated) to 1 (fully methylated). 
     Differential Methylation Analysis 
     Due to non-Gaussian distribution of the CpG methylation values, Wilcoxon Rank Sum tests were used to examine differences in median β-values between cases and controls in both phase I and phase II. To correct for multiple testing in phase I, q-values were used to represent the false discovery rate (FDR) (Storey and Tibshirani,  Proc. Natl. Acad. Sci. USA,  100(16):9440-5 (2003)). The CpGs with a FDR q-value≦0.05 level were considered significant. These CpGs were then candidates for phase II validation, where a p-value≦0.05 was considered significant. Bland-Altman plots were used to evaluate agreement between the two methylation assays in the 40 subjects assayed in both phase I and phase II. These plots allow evaluation of assay disagreement as a function of level of methylation (Bland and Altman,  Lancet,  1(8476):307-10 (1986)). 
     Prediction Model Building 
     To develop prediction models, likelihood cross-validated penalized logistic regression models, which implemented either an L1 penalty (Lasso) (Tibshirani,  J. Royal Statist. Soc. B,  58(1):267-88 (1996)) or an L2 penalty (Ridge) using the R package ‘penalized,’ were used (Goeman,  Biometrical Journal,  52(1):70-84 (2010)). A Lasso model (or L1 penalty) was utilized in phase I testing study because of its desirable feature for model selection, which has a minimal effect on associated CpG coefficients while setting the unassociated CpGs&#39; coefficients to zero. A Ridge regression model (or L2 penalty) that shrinks all coefficients to small values but not zeros was also considered for model building. The variable selection process is governed by a parameter that forces all coefficients to be shrunk near zero initially, then is gradually released to reduce the amount of shrinkage. The optimal value of this parameter is determined via cross validation. The Ridge model results were also compared to results from the Lasso model to hone the final model. 
     The final model identified through the penalized approaches was then fit as a generalized linear model (logistic regression) using the R package ‘glm’, in order to estimate the area under (AUC) the receiver operating characteristic (ROC) curve for each model. Models were fitted in both the testing set (phase I) and the validation set (phase II) separately with AUC reported for each model. In addition to the unadjusted model (only the CpGs), two more models were fitted, one that considered age, sex, and first degree family history as covariates and another that also considered ABO blood type (‘O’ vs ‘non-O’) as an additional covariate. ABO blood types were derived for a subset of patients which had GWAS genotype information (Petersen et al.,  Nat. Genet.,  42(3):224-8 (2010)) available. The phase II models were fit two ways. First, coefficients from phase I were held fixed and discrimination assessed. Second, since the assay platform changed from phase I to phase II, the models were fit allowing the coefficients to be re-estimated. 
     Identification of Differentially Methylated CpG Sites in Phase I 
     For phase I, 132 never-smoker patients with PaC and 60 never-smoker healthy controls were examined. Due to chemo- or radiation therapy before blood was drawn, 13 patients were excluded from this analysis. The methylation status (β values) of 1,505 CpG sites from leukocyte DNAs in the remaining 119 cases and 60 controls were evaluated (Table 2). Because significant methylation differences on the X chromosome exist between males and females, CpG sites on autosomes and sex chromosome were analyzed separately. These analyses identified significant differences at 110 CpG sites in 92 independent genes (FDR≦0.05). 109 of the 110 significant CpG sites were located on autosomes. Table 3 lists the 10 most significant CpG sites in the phase I study. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Subject demographics for Phases I and II. 
               
            
           
           
               
               
               
            
               
                   
                 Phase I 
                 Phase II 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                 Controls 
                 Cases 
                 P- 
                 Controls 
                 Cases 
                 P- 
               
               
                 Variable 
                 (N = 60) 
                 (N = 119) 
                 value 
                 (N = 215) 
                 (N = 173) 
                 value 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 Age 
                   
                   
                   
                   
                 1.00 
                   
                   
                   
                   
                 1.00 
               
               
                 ≦49 
                 3 
                 (5%) 
                 5 
                 (4%) 
                   
                 20 
                 (9%) 
                 15 
                 (9%) 
               
               
                 50-54 
                 4 
                 (7%) 
                 8 
                 (7%) 
                   
                 14 
                 (7%) 
                 10 
                 (6%) 
               
               
                 55-59 
                 7 
                 (12%) 
                 12 
                 (10%) 
                   
                 28 
                 (13%) 
                 21 
                 (12%) 
               
               
                 60-64 
                 7 
                 (12%) 
                 12 
                 (10%) 
                   
                 33 
                 (15%) 
                 26 
                 (15%) 
               
               
                 65-69 
                 12 
                 (20%) 
                 25 
                 (21%) 
                   
                 39 
                 (18%) 
                 33 
                 (19%) 
               
               
                 70-74 
                 11 
                 (18%) 
                 22 
                 (18%) 
                   
                 32 
                 (15%) 
                 22 
                 (13%) 
               
               
                 75-79 
                 11 
                 (18%) 
                 22 
                 (18%) 
                   
                 29 
                 (13%) 
                 29 
                 (17%) 
               
               
                 80-84 
                 3 
                 (5%) 
                 8 
                 (7%) 
                   
                 16 
                 (7%) 
                 14 
                 (8%) 
               
               
                 ≧85 
                 2 
                 (3%) 
                 5 
                 (4%) 
                   
                 4 
                 (2%) 
                 3 
                 (2%) 
               
               
                 Sex 
                   
                   
                   
                   
                 0.87 
                   
                   
                   
                   
                 0.90 
               
               
                 Female 
                 31 
                 (52%) 
                 60 
                 (50%) 
                   
                 108 
                 (50%) 
                 88 
                 (51%) 
               
               
                 Male 
                 29 
                 (48%) 
                 59 
                 (50%) 
                   
                 107 
                 (50%) 
                 85 
                 (49%) 
               
               
                 Family History of 
               
               
                 Pancreas Cancer 
               
               
                 (1 st  degree) 
               
               
                 No 
                 58 
                 (97%) 
                 104 
                 (87%) 
                 0.046 
                 196 
                 (91%) 
                 147 
                 (85%) 
                 0.06 
               
               
                 Yes 
                 2 
                 (3%) 
                 15 
                 (13%) 
                   
                 19 
                 (9%) 
                 26 
                 (15%) 
               
               
                 Smoking Status 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                 0.90 
               
               
                 Never Smokers 
                 60 
                 (100%) 
                 119 
                 (100%) 
                   
                 97 
                 (45%) 
                 77 
                 (45%) 
               
               
                 Ever Smokers 
                 0 
                 — 
                 0 
                 — 
                   
                 118 
                 (55%) 
                 96 
                 (55%) 
               
               
                 Stage of Pancreas 
               
               
                 Cancer 
               
               
                 Resectable 
                   
                   
                 31 
                 (26%) 
                   
                   
                   
                 58 
                 (34%) 
               
               
                 Locally 
                   
                   
                 45 
                 (38%) 
                   
                   
                   
                 59 
                 (34%) 
               
               
                 Advanced 
               
               
                 Metastatic 
                   
                   
                 43 
                 (36%) 
                   
                   
                   
                 56 
                 (32%) 
               
               
                 GWAS 
                   
                   
                   
                   
                 &lt;0.001 
                   
                   
                   
                   
                 0.028 
               
               
                 genotyping 
               
               
                 No 
                 34 
                 (57%) 
                 32 
                 (27%) 
                   
                 106 
                 (49%) 
                 66 
                 (38%) 
               
               
                 Yes 
                 26 
                 (43%) 
                 87 
                 (73%) 
                   
                 109 
                 (51%) 
                 107 
                 (62%) 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Top 10 most differentially methylated CpG sites 
               
               
                 in phase I and validation in phase II. 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Median β 
                 Median 
                 Difference 
                   
               
               
                 Illumina ID 
                 Control 
                 β Case 
                 (case-control) 
                 p value 
               
               
                   
               
            
           
           
               
               
            
               
                   
                 Phase I 
               
            
           
           
               
               
               
               
               
            
               
                 ITK_P114_F 
                 0.8337 
                 0.9006 
                 0.0669 
                     &lt;1E−10 
               
               
                 LCN2_P86_R 
                 0.5608 
                 0.4398 
                 −0.121 
                 2.00E−10 
               
               
                 ITK_E166_R 
                 0.8859 
                 0.9414 
                 0.0555 
                 5.00E−10 
               
               
                 PECAM1_E32_R 
                 0.2319 
                 0.1566 
                 −0.0753 
                 1.60E−09 
               
               
                 LMO2_E148_F 
                 0.3885 
                 0.2704 
                 −0.1181 
                 2.30E−09 
               
               
                 IL10_P348_F 
                 0.6026 
                 0.4597 
                 −0.1429 
                 2.50E−09 
               
               
                 LCK_E28_F 
                 0.8114 
                 0.8684 
                 0.057 
                 3.60E−09 
               
               
                 RUNX3_P247_F 
                 0.7837 
                 0.8672 
                 0.0835 
                 5.90E−09 
               
               
                 LMO2_P794_R 
                 0.3143 
                 0.2027 
                 −0.1116 
                 1.02E−08 
               
               
                 MMP14_P13_F 
                 0.4721 
                 0.3472 
                 −0.1249 
                 2.27E−08 
               
            
           
           
               
               
            
               
                   
                 Phase II 
               
            
           
           
               
               
               
               
               
            
               
                 ITK_P114_F 
                 0.846 
                 0.8898 
                 0.0438 
                     &lt;1E−10 
               
               
                 LCN2_P86_R 
                 0.591 
                 0.4993 
                 −0.0917 
                     &lt;1E−10 
               
               
                 ITK_E166_R 
                 0.8885 
                 0.9299 
                 0.0414 
                     &lt;1E−10 
               
               
                 PECAM1_E32_R 
                 0.2851 
                 0.2211 
                 −0.064 
                     &lt;1E−10 
               
               
                 LMO2_E148_F 
                 0.4969 
                 0.3904 
                 −0.1065 
                     &lt;1E−10 
               
               
                 IL10_P348_F 
                 0.7191 
                 0.6382 
                 −0.0809 
                     &lt;1E−10 
               
               
                 LCK_E28_F 
                 0.8593 
                 0.8999 
                 0.0406 
                     &lt;1E−10 
               
               
                 RUNX3_P247_F 
                 0.7528 
                 0.841 
                 0.0882 
                     &lt;1E−10 
               
               
                 LMO2_P794_R 
                 0.3754 
                 0.3027 
                 −0.0727 
                 6.00E−10 
               
               
                 MMP14_P13_F 
                 0.5694 
                 0.4807 
                 −0.0887 
                     &lt;1E−10 
               
               
                   
               
            
           
         
       
     
     To evaluate possible methylation changes during tumor progression, the methylation differences among three stages of PaC within this patient population, including 31 resectable, 45 locally advanced, and 43 metastatic cases, were examined. Although nine CpG sites showed a trend in association with clinical stages (p&lt;0.01) (Table 4), the data analysis did not reveal significant difference among the three stages (all CpG sites with FDR&gt;0.05). 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Top 10 most differentially methylated CpG sites among 3 clinical stages. 
               
            
           
           
               
               
               
            
               
                   
                 Mean β values 
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                 Gene 
                   
                 Locally 
                   
                 p 
                   
               
               
                 Illumina ID 
                 Name 
                 Resectable 
                 Advanced 
                 Metastatic 
                 value 
                 FDR 
               
               
                   
               
               
                 ZMYND10_P329_F 
                 ZMYND10 
                 0.045 
                 0.032 
                 0.019 
                 0.001 
                 0.722 
               
               
                 EPO_P162_R 
                 EPO 
                 0.077 
                 0.046 
                 0.068 
                 0.001 
                 0.722 
               
               
                 SCGB3A1_P103_R 
                 SCGB3A1 
                 0.004 
                 0.020 
                 0.004 
                 0.002 
                 0.722 
               
               
                 MEST_P4_F 
                 MEST 
                 0.042 
                 0.029 
                 0.061 
                 0.002 
                 0.722 
               
               
                 PWCR1_P357_F 
                 PWCR1 
                 0.917 
                 0.920 
                 0.890 
                 0.003 
                 0.722 
               
               
                 NTRK3_P636_R 
                 NTRK3 
                 0.009 
                 0.009 
                 0.004 
                 0.003 
                 0.722 
               
               
                 TIE1_E66_R 
                 TIE1 
                 0.203 
                 0.161 
                 0.153 
                 0.006 
                 1.000 
               
               
                 HLA_DPA1_P205_R 
                 HLA 
                 0.065 
                 0.041 
                 0.052 
                 0.007 
                 1.000 
               
               
                 EDNRB_P148_R 
                 EDNRB 
                 0.995 
                 0.995 
                 0.995 
                 0.009 
                 1.000 
               
               
                 COL1A2_P48_R 
                 COL1A2 
                 0.033 
                 0.023 
                 0.028 
                 0.011 
                 1.000 
               
               
                   
               
            
           
         
       
     
     Validation of Selected CpG Sites in Phase II 
     To validate the differentially methylated CpG sites identified in phase I within a larger number of patients and a broader range of demographic characteristics, a custom VeraCode methylation assay (Illumina, Inc.) was designed, and 96 of the 110 significant CpG sites were examined in 240 PaC cases and 240 matched controls. The 96 CpG sites were selected according to FDR values and median differences between cases and controls. Among the 480 subjects, 40 phase I subjects (20 cases and 20 controls) were included in order to compare the degree of agreement between the two methylation assays. Bland Altman plots (Bland and Altman,  Lancet,  1(8476):307-10 (1986)) showed little mean shift and constant variation of differences over the range of values ( FIG. 1 ), demonstrating reasonable agreement between the two assays. The two assays were significantly correlated as expected among all 96 CpG sites (mean Spearman correlation coefficient r=0.95). 
     Among the 220 PaC patients who were unique to phase II, 47 patients were treated before blood was drawn. The methylation levels between these 47 treated cases and 173 never-treated cases were compared to evaluate the effect of treatment on the methylation status of these selected CpG sites. Two CpG sites (TAL1_P817 F and CSF3_E242_R) exhibited nominal differences (p=0.001 and 0.025, respectively), although these results could be due to chance, given the large number of comparisons. Overall, a significant treatment effect on the methylation of these selected CpG sites was not observed. Similarly, no effect was attributable to smoking history. Of the remaining 220 controls, five additional controls were excluded due to inadequate quality, leaving 215 controls who were unique to phase II (Table 2). A total of 173 never-treated cases and 215 controls were used for analysis in phase II. The Wilcoxon Rank Sum Test identified a significant difference (p&lt;0.05) in 88 of the 96 selected CpGs. Importantly, all 88 of these validated CpG sites in phase II also exhibited the same direction of methylation change as phase I ( FIG. 2 ). Of those, 23 and 65 CpG sites demonstrated hypermethylation and hypomethylation in PaC patients, respectively. Table 3 lists the 10 most significant CpG sites in the phase II study (Table 5 contained statistics of the 96 CpG sites in both phases I and II). 
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Summary statistics (median (min, max) of the 96 significantly differentially 
               
               
                 methylated CpG sites by phase and case/control status. 
               
            
           
           
               
               
               
               
            
               
                 CpG 
                 Controls 
                 Cases 
                 p-value* 
               
               
                   
               
            
           
           
               
               
            
               
                   
                 Phase I 
               
            
           
           
               
               
               
               
            
               
                 ITK_P114_F 
                 83.37 (66.78, 92.51) 
                 90.06 (48.41, 97.28) 
                     &lt;1E−10 
               
               
                 LCN2_P86_R 
                 56.08 (32.4, 78.23)  
                 43.98 (5.71, 92.14)  
                 2.00E−10 
               
               
                 ITK_E166_R 
                 88.59 (71.81, 96.04) 
                 94.14 (50.72, 99.63) 
                 5.00E−10 
               
               
                 PECAM1_E32_R 
                 23.19 (12.47, 45.11) 
                 15.66 (1.16, 44.89)  
                 1.60E−09 
               
               
                 LMO2_E148_F 
                 38.85 (13.84, 64.09) 
                 27.04 (3.69, 77.03)  
                 2.30E−09 
               
               
                 IL10_P348_F 
                 60.26 (31.16, 79.7)  
                 45.97 (1.14, 88.97)  
                 2.50E−09 
               
               
                 LCK_E28_F 
                 81.14 (65.35, 90.81) 
                 86.84 (50.58, 96.12) 
                 3.60E−09 
               
               
                 RUNX3_P247_F 
                 78.37 (41.19, 91.2)  
                 86.72 (32.49, 96.71) 
                 5.90E−09 
               
               
                 LMO2_P794_R 
                 31.43 (10.99, 54.48) 
                 20.27 (0.43, 70.88)  
                 1.02E−08 
               
               
                 MMP14_P13_F 
                 47.21 (23.97, 77.03) 
                 34.72 (0.95, 81.85)  
                 2.27E−08 
               
               
                 CTLA4_E176_R 
                 90.98 (76.72, 97.1)  
                 94.27 (73.46, 99.51) 
                 2.43E−08 
               
               
                 SPI1_P48_F 
                  39.1 (13.89, 63.67) 
                 28.97 (0.46, 75.52)  
                 3.00E−08 
               
               
                 SLC22A18_P216_R 
                  35.3 (15.09, 60.06) 
                 24.88 (2.89, 71.26)  
                 3.22E−08 
               
               
                 RUNX3_P393_R 
                 82.38 (49.34, 92.26) 
                 88.77 (39.04, 97.27) 
                 3.27E−08 
               
               
                 TRIP6_P1090_F 
                 30.42 (8.07, 66.9)  
                 22.32 (3.25, 74.23)  
                 4.17E−08 
               
               
                 RARA_P1076_R 
                 22.76 (10.53, 47.06) 
                 16.02 (1.68, 48.24)  
                 8.70E−08 
               
               
                 PI3_P274_R 
                 75.78 (53.4, 91.48)  
                 65.96 (10.63, 95.55) 
                 8.85E−08 
               
               
                 ERCC3_P1210_R 
                 61.67 (38.27, 80.11) 
                 50.39 (18.34, 89.01) 
                 9.79E−08 
               
               
                 LCN2_P141_R 
                 72.86 (42.33, 87.3)  
                 64.16 (22.65, 94.55) 
                 1.16E−07 
               
               
                 RUNX3_E27_R 
                 89.46 (71.07, 98.1)  
                 93.35 (11.97, 99.64) 
                 1.87E−07 
               
               
                 TNFRSF1A_P678_F 
                 65.33 (47.4, 79.92)  
                 56.61 (23.05, 87.1)  
                 2.14E−07 
               
               
                 GFI1_P208_R 
                 19.6 (4.31, 46.99) 
                 12.75 (0, 36.77)    
                 2.28E−07 
               
               
                 CD9_P585_R 
                 33.34 (13.45, 50.34) 
                 26.51 (5.27, 56.39)  
                 2.32E−07 
               
               
                 MFAP4_P197_F 
                 22.82 (6.75, 55.77)  
                 16.41 (2.01, 56.84)  
                 2.96E−07 
               
               
                 AIM2_P624_F 
                 37.67 (17.86, 58.1)  
                 28.43 (2.03, 61.51)  
                 3.54E−07 
               
               
                 TRIP6_P1274_R 
                 43.57 (14.61, 74.3)  
                 32.95 (0.76, 76.92)  
                 5.36E−07 
               
               
                 CSF3R_P472_F 
                 33.44 (15.09, 55.24) 
                 23.61 (0.68, 69.4)  
                 6.91E−07 
               
               
                 ZAP70_P220_R 
                 28.41 (0.19, 47.82)  
                 35.31 (0, 59.95)    
                 8.47E−07 
               
               
                 GRB7_E71_R 
                 29.92 (11.39, 58.66) 
                 22.23 (5.27, 84.04)  
                 1.55E−06 
               
               
                 IFNG_E293_F 
                 76.11 (44.81, 90.56) 
                 82.66 (40.37, 99.16) 
                 1.57E−06 
               
               
                 LTA_P214_R 
                 79.91 (61.63, 93.55) 
                 85.5 (44.8, 94.89) 
                 2.13E−06 
               
               
                 SEPT9_P374_F 
                 24.56 (11.19, 48.39) 
                 17.19 (2.52, 59.09)  
                 2.55E−06 
               
               
                 CD9_P504_F 
                 13.81 (1.88, 28.33)  
                 8.02 (0.54, 39.44) 
                 3.19E−06 
               
               
                 SPI1_E205_F 
                 20.85 (1.87, 42.24)  
                 15.34 (1.34, 49.21)  
                 4.34E−06 
               
               
                 ZMYND10_P329_F 
                 4.65 (0, 21)     
                 2.35 (0, 18.04)   
                 4.53E−06 
               
               
                 CSF3R_P8_F 
                 20.73 (1.86, 41.89)  
                 14.64 (0.77, 42.8)  
                 4.54E−06 
               
               
                 CSF3_E242_R 
                 66.58 (49.37, 81.52) 
                 59.27 (21.44, 90.38) 
                 5.10E−06 
               
               
                 PECAM1_P135_F 
                 18.55 (0.47, 45.36)  
                 11.37 (0.19, 33.84)  
                 5.10E−06 
               
               
                 EMR3_E61_F 
                 15.65 (5.25, 34.99)  
                 11.63 (0.24, 41.7)  
                 6.43E−06 
               
               
                 STAT5A_P704_R 
                 16.81 (5.15, 46.21)  
                 12.17 (0.28, 41.17)  
                 6.52E−06 
               
               
                 MMP9_P189_F 
                 31.53 (1.9, 56.05)  
                 22.65 (0.4, 49.69)  
                 7.01E−06 
               
               
                 SLC5A5_E60_F 
                 45.17 (21.04, 74.82) 
                 37.67 (8.07, 76.8)  
                 8.56E−06 
               
               
                 CRIP1_P874_R 
                 13.49 (4.42, 29.09)  
                 10.29 (1.06, 25.26)  
                 1.33E−05 
               
               
                 SYK_P584_F 
                 38.57 (0.24, 59.13)  
                 30.97 (0.67, 68.67)  
                 1.34E−05 
               
               
                 APBA2_P227_F 
                 94.88 (84.03, 99.63) 
                 97.09 (84.71, 99.65) 
                 1.38E−05 
               
               
                 TM7SF3_P1068_R 
                 56.68 (23.59, 82.45) 
                 46.79 (16.31, 87.94) 
                 1.59E−05 
               
               
                 RAB32_E314_R 
                 1.98 (0.27, 11.26) 
                 0.91 (0, 9.5)    
                 1.72E−05 
               
               
                 TAL1_P817_F 
                 21.45 (0, 49.38)    
                 14.26 (0, 40.73)    
                 1.74E−05 
               
               
                 IGFBP5_P9_R 
                 12.66 (0.07, 29.2)  
                 8.85 (0, 27.87)   
                 1.90E−05 
               
               
                 HPN_P374_R 
                 9.66 (0.26, 23.76) 
                 7.17 (0, 26.79)   
                 2.53E−05 
               
               
                 RHOH_P953_R 
                 97.62 (72.16, 99.47) 
                 99.03 (76.43, 99.6)  
                 3.49E−05 
               
               
                 MPL_P62_F 
                 29.8 (2.41, 58.43) 
                 22.88 (0, 55.22)    
                 3.54E−05 
               
               
                 PADI4_E24_F 
                 17.86 (0.32, 38.35)  
                 11.31 (0, 41.96)    
                 3.83E−05 
               
               
                 AIM2_E208_F 
                  96.3 (80.67, 99.46) 
                 97.97 (80.23, 99.54) 
                 4.20E−05 
               
               
                 KRT1_P798_R 
                 83.01 (66.54, 93.3)  
                 85.93 (68.78, 93.73) 
                 4.20E−05 
               
               
                 GPR116_P850_F 
                 96.05 (89.31, 98.99) 
                 97.09 (90.05, 99.25) 
                 4.26E−05 
               
               
                 TIE1_E66_R 
                 21.18 (0.91, 42.26)  
                 15.33 (0.55, 51.7)  
                 4.79E−05 
               
               
                 HGF_E102_R 
                 19.94 (7.37, 42.41)  
                 15.13 (0.53, 50.53)  
                 5.46E−05 
               
               
                 PADI4_P1011_R 
                  69.9 (51.57, 81.11) 
                 73.91 (51.55, 88.23) 
                 5.53E−05 
               
               
                 GSTM2_P453_R 
                 59.15 (40.51, 83.4)  
                 53.81 (25.36, 79.44) 
                 6.80E−05 
               
               
                 NOTCH4_E4_F 
                 15.25 (1.14, 41.15)  
                 9.84 (0.61, 35.21) 
                 6.89E−05 
               
               
                 MMP8_E89_R 
                 64.58 (42.74, 83.76) 
                 55.81 (0, 85.68)    
                 7.64E−05 
               
               
                 HIC_1_sEq_48_S103_R 
                 27.61 (0.09, 70.36)  
                 19.73 (0, 80.7)    
                 9.84E−05 
               
               
                 IFNG_P459_R 
                 85.46 (65.44, 97.27) 
                 88.28 (53.34, 96.99) 
                 1.06E−04 
               
               
                 EPHA2_P203_F 
                 43.85 (25.91, 67.36) 
                 36.39 (6.07, 77.13)  
                 1.07E−04 
               
               
                 CD82_P557_R 
                 19.56 (0, 51.55)    
                 13.07 (0, 43.55)    
                 1.08E−04 
               
               
                 VAMP8_P241_F 
                 31.69 (11.54, 50.58) 
                 24.36 (0.94, 54.16)  
                 1.25E−04 
               
               
                 CD86_P3_F 
                 12.46 (0.32, 40.34)  
                 9.46 (0.29, 32.83) 
                 1.72E−04 
               
               
                 DHCR24_P652_R 
                 44.87 (14.92, 62.58) 
                   39 (14.67, 66.69) 
                 1.76E−04 
               
               
                 SPARC_P195_F 
                 14.27 (2.87, 32.85)  
                 11.31 (0.52, 39.17)  
                 1.83E−04 
               
               
                 IL1RN_P93_R 
                  94.2 (87.08, 99.47) 
                 95.59 (85.25, 99.49) 
                 2.17E−04 
               
               
                 IFNGR2_P377_R 
                 21.62 (7.95, 48.7)  
                 16.2 (0, 68.34)   
                 2.17E−04 
               
               
                 CARD15_P302_R 
                 9.02 (0.6, 28.97)  
                 5.96 (0, 27.3)    
                 2.69E−04 
               
               
                 BCL2L2_P280_F 
                 7.89 (0, 21.29)   
                 4.95 (0, 25.19)   
                 2.78E−04 
               
               
                 SLC22A18_P472_R 
                 83.47 (72.01, 94.27) 
                 80.33 (34.95, 93.43) 
                 3.56E−04 
               
               
                 CSF1R_E26_F 
                 66.55 (30.32, 88.93) 
                 58.76 (16.56, 86.36) 
                 4.34E−04 
               
               
                 CLDN4_P1120_R 
                 89.62 (78.16, 96.19) 
                 91.19 (76.74, 97.54) 
                 4.54E−04 
               
               
                 GRB7_P160_R 
                 60.07 (33.43, 80.13) 
                 51.85 (14.14, 95.94) 
                 6.39E−04 
               
               
                 AXL_E61_F 
                 7.82 (0, 23.86)   
                 5.17 (0, 42)     
                 7.93E−04 
               
               
                 ALOX12_E85_R 
                 47.85 (7.84, 90.76)  
                 37.95 (2.82, 84.99)  
                 7.98E−04 
               
               
                 TFPI2_P152_R 
                 8.68 (1.16, 25.69) 
                 7.23 (0, 19.55)   
                 8.43E−04 
               
               
                 AGXT_P180_F 
                 84.04 (54.05, 94.35) 
                 78.61 (30.32, 95.02) 
                 8.90E−04 
               
               
                 IL10_P85_F 
                 16.33 (2.21, 31.74)  
                 11.98 (0.6, 28.58)  
                 1.04E−03 
               
               
                 KCNK4_E3_F 
                 30.96 (16.67, 58.04) 
                 26.78 (12.25, 65.38) 
                 1.16E−03 
               
               
                 JAK3_P1075_R 
                 69.62 (43.74, 86.14) 
                 64.45 (39.85, 85.81) 
                 1.31E−03 
               
               
                 IL6_P213_R 
                 4.39 (0.3, 16.26)  
                 3.24 (0, 12.35)   
                 1.36E−03 
               
               
                 NOTCH4_P938_F 
                 77.66 (57.82, 90.79) 
                  80.6 (58.86, 92.06) 
                 1.36E−03 
               
               
                 PTPN6_P282_R 
                 17.03 (0, 39.81)    
                 12.82 (0, 52.14)    
                 1.39E−03 
               
               
                 MATK_P190_R 
                 10.43 (0.92, 26.11)  
                 6.55 (0, 40.44)   
                 1.52E−03 
               
               
                 CEACAM1_P44_R 
                 7.92 (2.35, 21.58) 
                 5.91 (0.12, 17.51) 
                 1.62E−03 
               
               
                 CASP10_P334_F 
                 12.55 (0.26, 42.94)  
                 9.29 (0, 39.33)   
                 1.66E−03 
               
               
                 FGF1_P357_R 
                 95.37 (87.76, 99.49) 
                 96.51 (86.05, 99.63) 
                 2.14E−03 
               
               
                 IL17RB_E164_R 
                 10.41 (0.69, 28.02)  
                 7.84 (0, 29.55)   
                 2.21E−03 
               
               
                 CPA4_E20_F 
                  83.5 (64.39, 93.13) 
                 86.45 (59.8, 99.29)  
                 2.28E−03 
               
               
                 PTHR1_P258_F 
                 62.11 (31.07, 81.92) 
                 66.79 (38.33, 85.98) 
                 2.50E−03 
               
               
                 ESR1_P151_R 
                 9.47 (0.17, 28.16) 
                 7.72 (0, 26.14)   
                 3.44E−03 
               
            
           
           
               
               
            
               
                   
                 Phase II 
               
            
           
           
               
               
               
               
            
               
                 ITK_P114_F 
                 84.6 (4.07, 94.97) 
                 88.98 (65.48, 95.66) 
                     &lt;1E−10 
               
               
                 LCN2_P86_R 
                  59.1 (25.07, 89.12) 
                 49.93 (13.42, 87.19) 
                     &lt;1E−10 
               
               
                 ITK_E166_R 
                 88.85 (75.13, 97.07) 
                 92.99 (66.52, 97.68) 
                     &lt;1E−10 
               
               
                 PECAM1_E32_R 
                 28.51 (3.17, 58.59)  
                 22.11 (7.07, 47.24)  
                     &lt;1E−10 
               
               
                 LMO2_E148_F 
                 49.69 (12.63, 66.96) 
                 39.04 (9.57, 74.81)  
                     &lt;1E−10 
               
               
                 IL10_P348_F 
                 71.91 (30.76, 84.99) 
                 63.82 (18.98, 86.99) 
                     &lt;1E−10 
               
               
                 LCK_E28_F 
                 85.93 (66.63, 94.24) 
                 89.99 (69.32, 95.97) 
                     &lt;1E−10 
               
               
                 RUNX3_P247_F 
                 75.28 (46.66, 92.97) 
                 84.1 (44.68, 94.7) 
                     &lt;1E−10 
               
               
                 LMO2_P794_R 
                 37.54 (7.76, 66)    
                 30.27 (4.33, 67.54)  
                 6.00E−10 
               
               
                 MMP14_P13_F 
                 56.94 (1.91, 75.33)  
                 48.07 (14.03, 82.2)  
                     &lt;1E−10 
               
               
                 CTLA4_E176_R 
                 90.42 (70.84, 96.69) 
                 93.6 (75.8, 97.07) 
                     &lt;1E−10 
               
               
                 SPI1_P48_F 
                 0 (0, 65.26) 
                 0 (0, 66.39) 
                 8.73E−01 
               
               
                 SLC22A18_P216_R 
                 45.39 (3.56, 67.22)  
                 37.63 (11.09, 65.12) 
                     &lt;1E−10 
               
               
                 RUNX3_P393_R 
                 85.91 (60.74, 94.14) 
                 90.52 (59.59, 96.07) 
                     &lt;1E−10 
               
               
                 TRIP6_P1090_F 
                 49.69 (15.94, 78.31) 
                 42.87 (7.49, 71.8)  
                 7.20E−09 
               
               
                 RARA_P1076_R 
                 15.22 (2.19, 34.67)  
                 10.9 (2.49, 31.5)  
                     &lt;1E−10 
               
               
                 PI3_P274_R 
                 76.46 (11.61, 86.93) 
                 68.74 (33.03, 89.85) 
                     &lt;1E−10 
               
               
                 ERCC3_P1210_R 
                 63.04 (34.49, 76.41) 
                 53.35 (20.9, 81.21)  
                     &lt;1E−10 
               
               
                 LCN2_P141_R 
                 70.29 (6.04, 90.27)  
                 63.03 (26.51, 90.6)  
                     &lt;1E−10 
               
               
                 RUNX3_E27_R 
                 85.68 (59.92, 96.29) 
                 90.88 (64.9, 97.41)  
                     &lt;1E−10 
               
               
                 TNFRSF1A_P678_F 
                 69.85 (28.76, 83.56) 
                 62.92 (32.87, 84.15) 
                     &lt;1E−10 
               
               
                 GFI1_P208_R 
                 27.99 (2.92, 57.92)  
                 21.48 (2.67, 51.52)  
                     &lt;1E−10 
               
               
                 CD9_P585_R 
                 29.61 (4.66, 54.39)  
                 25.49 (12.88, 46.71) 
                     &lt;1E−10 
               
               
                 MFAP4_P197_F 
                 20.52 (9.22, 37.18)  
                 15.63 (5.54, 32.33)  
                     &lt;1E−10 
               
               
                 AIM2_P624_F 
                 24.47 (2.07, 47.94)  
                 18.36 (4.35, 43.95)  
                     &lt;1E−10 
               
               
                 TRIP6_P1274_R 
                 0 (0, 74.89) 
                 0 (0, 72.24) 
                 1.19E−01 
               
               
                 CSF3R_P472_F 
                 35.13 (12.28, 53.48) 
                 27.56 (6.94, 61.54)  
                     &lt;1E−10 
               
               
                 ZAP70_P220_R 
                 47.65 (2.73, 76.92)  
                 52.39 (33.54, 75.02) 
                 1.50E−09 
               
               
                 GRB7_E71_R 
                 36.02 (1.92, 61.12)  
                 29.79 (6.77, 62.93)  
                  l.00E−09 
               
               
                 IFNG_E293_F 
                 70.66 (21.85, 87.7)  
                 77.72 (39.38, 91.66) 
                     &lt;1E−10 
               
               
                 LTA_P214_R 
                 81.58 (59.26, 94.06) 
                 86.32 (57.97, 94.15) 
                     &lt;1E−10 
               
               
                 SEPT9_P374_F 
                 0 (0, 56.25) 
                 0 (0, 58.96) 
                 7.74E−02 
               
               
                 CD9_P504_F 
                 31.4 (1.94, 58.89) 
                 23.61 (2.66, 54.55)  
                     &lt;1E−10 
               
               
                 SPI1_E205_F 
                 46.01 (1.94, 68.8)  
                 38.93 (2.04, 67.89)  
                     &lt;1E−10 
               
               
                 ZMYND10_P329_F 
                 8.93 (2.5, 36.09)  
                 7.42 (1.79, 27.24) 
                 3.35E−07 
               
               
                 CSF3R_P8_F 
                 27.34 (3.84, 54.47)  
                 21.74 (5.7, 52.03)  
                     &lt;1E−10 
               
               
                 CSF3_E242_R 
                 61.98 (40.79, 78.17) 
                 56.43 (33.01, 78.13) 
                     &lt;1E−10 
               
               
                 PECAM1_P135_F 
                 14.99 (3.05, 32.67)  
                 11.05 (3.26, 25.28)  
                     &lt;1E−10 
               
               
                 EMR3_E61_F 
                 20.71 (6.49, 38.41)  
                 15.09 (3.15, 38.97)  
                     &lt;1E−10 
               
               
                 STAT5A_P704_R 
                 30.55 (3.94, 52.04)  
                 22.97 (6.02, 52.51)  
                     &lt;1E−10 
               
               
                 MMP9_P189_F 
                 37.54 (3.11, 57.08)  
                 32.85 (7.59, 55.08)  
                 1.30E−09 
               
               
                 SLC5A5_E60_F 
                 51.28 (27.1, 74.6)  
                 47.82 (9.37, 68.78)  
                 7.29E−06 
               
               
                 CRIP1_P874_R 
                 20.02 (2.69, 42.34)  
                 17.73 (8.46, 34.07)  
                 2.48E−05 
               
               
                 SYK_P584_F 
                 44.33 (4.94, 64.17)  
                 37.47 (2.48, 68.35)  
                     &lt;1E−10 
               
               
                 APBA2_P227_F 
                 92.19 (84.38, 97.59) 
                 93.86 (74.03, 97.18) 
                     &lt;1E−10 
               
               
                 TM7SF3_P1068_R 
                 54.8 (24.74, 84.6) 
                 46.58 (9.06, 71.14)  
                     &lt;1E−10 
               
               
                 RAB32_E314_R 
                 3.97 (2.42, 15.73) 
                 3.82 (2.18, 10.52) 
                 5.02E−02 
               
               
                 TAL1_P817_F 
                 27.29 (5.59, 46.43)  
                 25.55 (9.32, 43.64)  
                 3.56E−02 
               
               
                 IGFBP5_P9_R 
                 21.5 (3.54, 43.93) 
                 18.17 (3.12, 48.74)  
                 3.03E−07 
               
               
                 HPN_P374_R 
                 20.25 (5.94, 66.95)  
                 16.97 (7.79, 77.97)  
                 3.46E−07 
               
               
                 RHOH_P953_R 
                 92.75 (63.97, 96.75) 
                 94.02 (77.66, 96.71) 
                 2.00E−10 
               
               
                 MPL_P62_F 
                 34.54 (4.53, 66.72)  
                 28.09 (9.17, 53.73)  
                     &lt;1E−10 
               
               
                 PADI4_E24_F 
                 24.96 (2.95, 47.22)  
                 20.03 (2.9, 47.69)  
                     &lt;1E−10 
               
               
                 AIM2_E208_F 
                 94.45 (77.86, 97.47) 
                 95.66 (83.76, 98.08) 
                     &lt;1E−10 
               
               
                 KRT1_P798_R 
                  89.5 (71.75, 93.92) 
                 91.48 (75.18, 94.92) 
                     &lt;1E−10 
               
               
                 GPR116_P850_F 
                 95.47 (90.14, 97.05) 
                 96.11 (92.96, 97.1)  
                     &lt;1E−10 
               
               
                 TIE1_E66_R 
                 29.29 (2.4, 51.91)  
                 23.94 (2.85, 47.27)  
                     &lt;1E−10 
               
               
                 HGF_E102_R 
                 23.18 (1.86, 41.47)  
                 19.87 (2.6, 39.95)  
                 1.12E−06 
               
               
                 PADI4_P1011_R 
                 76.61 (9.64, 87.91)  
                 81.19 (55.69, 89.2)  
                     &lt;1E−10 
               
               
                 GSTM2_P453_R 
                 64.77 (39.09, 86.35) 
                  62.7 (40.83, 76.29) 
                 9.83E−03 
               
               
                 NOTCH4_E4_F 
                 20.61 (6.52, 44.05)  
                 16.87 (3.08, 33.64)  
                 6.00E−10 
               
               
                 MMP8_E89_R 
                 70.66 (6.82, 86.44)  
                 65.54 (32.82, 78.69) 
                     &lt;1E−10 
               
               
                 HIC_l_sEq_48_S103_R 
                 19.78 (7.67, 47.09)  
                 18.19 (3.33, 55.88)  
                 3.11E−02 
               
               
                 IFNG_P459_R 
                 89.86 (64.27, 96.86) 
                 92.57 (66.81, 97.08) 
                     &lt;1E−10 
               
               
                 EPHA2_P203_F 
                 74.53 (3.66, 89.34)  
                 67.54 (30.76, 87.52) 
                     &lt;1E−10 
               
               
                 CD82_P557_R 
                     22 (2.73, 60.61) 
                 17.48 (2.62, 39)    
                 5.40E−09 
               
               
                 VAMP8_P241_F 
                 40.17 (2.11, 63.54)  
                 34.37 (14.11, 52.08) 
                     &lt;1E−10 
               
               
                 CD86_P3_F 
                 15.87 (2.39, 30.32)  
                 13.49 (2.9, 28.27)  
                 2.22E−05 
               
               
                 DHCR24_P652_R 
                 48.39 (23.78, 74.34) 
                 41.86 (17.02, 67.4)  
                     &lt;1E−10 
               
               
                 SPARC_P195_F 
                 14.5 (3.93, 36.44) 
                 13.39 (5.63, 37.38)  
                 7.57E−06 
               
               
                 IL1RN_P93_R 
                  94.3 (85.78, 97.34) 
                 95.28 (90.71, 97.45) 
                     &lt;1E−10 
               
               
                 IFNGR2_P377_R 
                     29 (2.85, 53.14) 
                 22.53 (3.82, 41.23)  
                     &lt;1E−10 
               
               
                 CARD15_P302_R 
                 19.22 (3.24, 45.09)  
                 14.16 (3.66, 36.68)  
                 5.70E−09 
               
               
                 BCL2L2_P280_F 
                 18.13 (2.77, 54.1)  
                 16.71 (2.46, 44.21)  
                 3.81E−03 
               
               
                 SLC22A18_P472_R 
                  86.1 (69.16, 93.29) 
                 84.96 (73.83, 91.2)  
                 6.48E−04 
               
               
                 CSF1R_E26_F 
                 74.92 (25.36, 90.91) 
                 70.85 (39.78, 91.21) 
                 3.45E−07 
               
               
                 CLDN4_P1120_R 
                 91.31 (73.07, 95.82) 
                 92.64 (77.49, 95.59) 
                     &lt;1E−10 
               
               
                 GRB7_P160_R 
                 72.13 (41.09, 88.74) 
                 71.11 (13.96, 92.63) 
                 1.56E−01 
               
               
                 AXL_E61_F 
                 15.47 (2.5, 40.29)  
                 13.19 (3, 40.16)    
                 2.54E−03 
               
               
                 ALOX12_E85_R 
                 54.6 (6.87, 85.62) 
                 51.44 (7.44, 88.52)  
                 6.15E−02 
               
               
                 TFPI2_P152_R 
                 13.78 (2.43, 29.91)  
                 13.21 (2.21, 29.07)  
                 1.97E−01 
               
               
                 AGXT_P180_F 
                 77.55 (44.53, 90.06) 
                 74.85 (33.53, 87.81) 
                 1.03E−03 
               
               
                 IL10_P85_F 
                 21.04 (2.06, 38.09)  
                 16.05 (5.04, 46.92)  
                     &lt;1E−10 
               
               
                 KCNK4_E3_F 
                 0 (0, 89.11) 
                 0 (0, 63.18) 
                 7.74E−01 
               
               
                 JAK3_P1075_R 
                 70.21 (46.11, 85.05) 
                 68.02 (43.53, 87.34) 
                 5.43E−03 
               
               
                 IL6_P213_R 
                 10.48 (2.53, 33.05)  
                 7.87 (2.03, 25.36) 
                 1.33E−08 
               
               
                 NOTCH4_P938_F 
                 77.74 (44, 87.97)   
                 82.18 (64.28, 89.48) 
                     &lt;1E−10 
               
               
                 PTPN6_P282_R 
                 23.29 (3.67, 71.66)  
                 18.9 (2.67, 72.99) 
                 1.96E−05 
               
               
                 MATK_P190_R 
                 10.37 (3.76, 38.93)  
                 8.33 (2.91, 26.71) 
                 1.35E−06 
               
               
                 CEACAM1_P44_R 
                 10.06 (3.35, 25.72)  
                 8.58 (2.81, 24.96) 
                 4.35E−04 
               
               
                 CASP10_P334_F 
                 22.91 (10.21, 49.38) 
                 21.77 (9.58, 47.71)  
                 2.88E−02 
               
               
                 FGF1_P357_R 
                 93.66 (77.45, 96.31) 
                 94.92 (84.85, 97.12) 
                     &lt;1E−10 
               
               
                 IL17RB_E164_R 
                 11.97 (2.77, 43.06)  
                 12.35 (2.96, 37.44)  
                 7.60E−01 
               
               
                 CPA4_E20_F 
                 88.05 (56.56, 93.9)  
                 90.57 (68.86, 97.31) 
                 1.00E−10 
               
               
                 PTHR1_P258_F 
                 64.33 (3.69, 83.88)  
                 68.73 (35.03, 83.62) 
                 4.00E−10 
               
               
                 ESR1_P151_R 
                 10.92 (2.9, 25.71)  
                 8.85 (2.34, 24.42) 
                 7.80E−09 
               
               
                   
               
            
           
         
       
     
     Building and Validation of the Prediction Model 
     To build prediction models based on phase I data, 43 of the 96 CpG sites that showed less than 5% median β differences between cases and controls or p-value≧0.001 (FDR&gt;0.007) in phase I were excluded. These filter criteria were set for the following technical considerations. First, CpG sites with smaller methylation differences are prone to laboratory error due to technical limitations. Second, CpG sites with less significant p-values are less likely to be replicated in future studies. Based on 53 remaining CpG sites, models were built using L1 and L2 penalties as described above using the phase I data. 
     An effective model was chosen based on criteria of ROC AUC and parsimony. This model was then tested using the phase II data without the 40 subjects assayed in both phases for the agreement study. When considering all cases and all controls, a panel of five CpG sites (Model I: IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817) was identified. These five CpG sites were the first five CpGs to enter and remain in the Lasso model and also had the five largest coefficients from the Ridge model. This five CpG-only model exhibited good discrimination between patients and controls (c-statistic=0.85 in phase I and 0.76 in phase II) based on the logistic regression model. When including covariates in the logistic regression model (age, sex, 1 st  degree of family history of PaC, and ABO blood type), the discrimination was improved in phase I (c-statistic=0.89), but decreased in phase II (c-statistic=0.72). When re-estimating coefficients in phase II (re-fitting), the discrimination was improved, but not dramatically (c-statistic=0.77 for five CpGs only, 0.77 after inclusion of covariates) (Table 6). When including resectable patients only and all controls, one CpG site (Model II: LCN2_P86) was identified that appeared to discriminate for resectable disease (c-statistic=0.78 in phase I and 0.74 in phase II). 
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Methylation-based predication models and Area Under the ROC Curve (AUC). 
               
            
           
           
               
               
               
               
            
               
                   
                 Phase I 
                 Phase II 
                 Phase II - Re-fit 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 CpG + 
                   
                   
                 CpG + 
                   
                   
                 CpG + 
               
               
                 Mod- 
                 CpG 
                 CpGs 
                 CpG + 
                 Covariates* + 
                 CpGs 
                 CpG + 
                 Covariates* + 
                 CpGs 
                 CpG + 
                 Covariates* + 
               
               
                 els 
                 Illumina ID 
                 only 
                 Covariates* 
                 ABO** 
                 only 
                 Covariates* 
                 ABO** 
                 only 
                 Covariates* 
                 ABO** 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 All Cases and All 
                 60 controls, 119 cases 
                 215 controls, 173 cases 
                 215 controls, 173 cases 
               
               
                 Controls 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 I 
                 IL10_P348 
                 0.85 
                 0.86 
                 0.89 
                 0.76 
                 0.75 
                 0.72 
                 0.77 
                 0.77 
                 0.77 
               
               
                   
                 LCN2_P86 
               
               
                   
                 ZAP70_P220 
               
               
                   
                 AIM2_P624 
               
               
                   
                 TAL1_P817 
               
            
           
           
               
               
               
               
            
               
                 Resectable Cases and 
                 60 controls, 31 cases  
                 215 controls, 58 cases  
                 215 controls, 58 cases  
               
               
                 All Controls 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 II 
                 LCN2_P86 
                 0.78 
                 0.79 
                 0.82 
                 0.74 
                 0.67 
                 0.64 
                 0.73 
                 0.73 
                 0.73 
               
               
                   
               
               
                 *Covariates includes age, sex, 1st degree Family history of PaC. 
               
               
                 **ABO-blood type of O and non-O. 
               
            
           
         
       
     
     The results provided herein demonstrate that epigenetic variation in leukocyte DNA, manifested by reproducible methylation differences, can be used as an early diagnostic marker for differentiating between pancreatic cancer patients and humans without pancreatic cancer (e.g., healthy humans). For example, a panel that includes the IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, and TAL1_P817 CpG methylation sites can be used to identify pancreatic cancer patients. The results provided herein also demonstrate that the LCN2_P86 CpG methylation site is capable of identifying human patients with resectable pancreatic cancer. 
     Other Embodiments  
     It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.