We identified eight loci where CNV is significantly associated with HCC. Six of these appear to be germline CNVs. The other two, however, involve T-cell receptor

loci, which PD 332991 are known to undergo recombination in peripheral blood lymphocytes, the source of DNA for our study. Of the six loci showing germline CNV, the one exhibiting the strongest association with HCC is a small region of chromosome 1p36.33 that contains no known or predicted genes. In this case, low copy number correlates with increased risk for both HCC (unadjusted P = 5.94 × 10−16 for Stage 1, P = 1.11 × 10−10 for Stage 2; Table 1) and LC (unadjusted P = 6.03 × 10−9 for combined Stage 1 and Stage 2; Table 2). The five other regions for which CNV is associated AZD2281 with HCC contain the genes KNG1 (3q27.3); C4orf29 and LARP2 (4q28.2); ALDH7A1, PHAX, C5orf48, and LMNB1 (5q23.2); SRPK2 and PUS7 (7q22.2); and TMPO (12q23.1). Low copy number at all five of these loci is more

frequent in controls than HCC patients (Table 1). We observed no statistically significant association between CNV at these five loci and LC (Table 2). Additionally, none of these loci show significant differences between LC and HCC. Among the loci showing association of CNV with HCC, the strongest association is seen at the TRG@ and TRA@. In both cases low copy number is more frequent in controls than cases. In HCC versus controls, TRG@ shows an unadjusted P of 3.16 × 10−21 in the Stage 1 training HSP90 set and P = 1.85 × 10−28 in the Stage 2 testing set; TRA@ has an unadjusted P = 1.94 × 10−16 in Stage 1 and P = 6.24 × 10−28 in Stage 2 (Table 1). We validated these findings using an independent platform by performing a TaqMan assay (t test P = 2.86 × 10−18 for TRA@; P = 3.56 × 10−26 for TRG@ for combined Stage 1 and Stage 2 samples; Supporting Table S9). CNV at the TRG@ and TRA@ loci also differs significantly between control and LC individuals (unadjusted P of 5.66 × 10−12 and 3.17 × 10−13, respectively, in combined Stage 1 and Stage 2 samples; Table 2). As is seen in HCC, low copy

number is more frequent in control than LC individuals. To confirm our proposal that the observed CNV at TRA@ and TRG@ reflects somatic genomic rearrangement at these loci that occurs in normal T lymphocytes, we inspected publicly accessible CNV data at these T-cell receptor loci in B cells. Because B cells do not exhibit TCR rearrangement, they should be diploid at the TRA@ and TRG@ loci. As expected, neither locus shows CNV in publicly accessible HapMap genotype data, which were generated using DNA isolated from B-cell lymphoblastoid cell lines established at the Centre d’Etude du Polymorphisme Humain (CEPH).17 We observe no significant association between CNV at the T-cell receptor loci and hepatitis virus status in the cases where viral status is known in the current study population (Supporting Table S4).