Deep resequencing of 131 Crohn's disease associated genes in pooled DNA confirmed three reported variants and identified eight novel variants

Objective: Genome wide association studies (GWAS) and meta-analyses for Crohn's disease (CD) have not fully explained the heritability of CD, suggesting that additional loci are yet to be found and that the known loci may contain high effect rare risk variants that have thus far gone undetected by GWAS. While the cost of deep sequencing remains too high to analyse many samples, targeted sequencing of pooled DNA samples allows the efficient and cost effective capture of all variations in a target region. Design: We performed pooled sequencing in 500 Korean CD cases and 1000 controls to evaluate the coding exon and 50 and 30 untranslated regions of 131 CD associated genes. The identified genetic variants were validated using genotyping in an independent set of 500 CD cases and 1000 controls. Results: Pooled sequencing identified 30 common/low single nucleotide variants (SNVs) in 12 genes and 3 rare SNVs in 3 genes. Our results confirmed a significant association of CD with the following previously reported risk loci: rs3810936 in TNFSF15 (OR=1.83, p<2.2×10^-16), rs76418789 in IL23R (OR=0.47, p=1.14×10^-8) and rs2241880 in AT G1 6L1 (OR=1.30, p=5.28×10^-6). In addition, novel loci were identified in TNFSF8 (rs3181374, OR=1.53, p=1.03×10^-14), BTNL2 (rs28362680, OR=1.47, p=9.67×10^-11), HLA-DQA2 (rs3208181, OR=1.36, p=4.66×10^-6), STAT3 (rs1053004, OR=1.29, p=2.07×10^-5), NFKBIA (rs2273650, OR=0.80, p=3.93×10^-4), NKX2-3 (rs888208, OR=0.82, p=6.37×10^-4) and DNAH12 (rs4462937, OR=1.13, p=3.17×10^-2). A novel rare SNV, rs200735402 in CARD9, was shown to have a protective effect (OR=0.09, p=5.28×10^-5)). Conclusions: Our deep resequencing of 131 CD associated genes confirmed 3 reported risk loci and identified 8 novel risk loci for CD in Koreans, providing new insights into the genetic architecture of CD.