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

Inflammatory bowel disease

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

Sung Noh Hong1*,
Changho Park2,3*,
Soo Jung Park4,
Chang Kyun Lee5,
Byong Duk Ye6,
You Sun Kim7,
Seungbok Lee2,3,8,
Jeesoo Chae2,3,
Jong-Il Kim2,3,8,9†,
Young-Ho Kim1†,
IBD Study Group of the Korean Association for the Study of Intestinal Diseases (KASID)
1Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
2Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
3Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea
4 Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
5Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
6Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Centre, University of Ulsan College of Medicine
7Department of Internal Medicine, Seoul Paik Hospital, Inje University College of Medicine, Seoul, Korea
8Medical Research Center, Genomic Medicine Institute (GMI), Seoul National University, Seoul, Korea
9Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
Correspondence to Professor Y-H Kim, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea; younghokim{at}skku.eduProfessor J-I Kim, Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; jongil{at}snu.ac.kr

Abstract

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 5′ and 3′ 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 ATG16L1 (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.

GENETIC POLYMORPHISMS
CROHN'S DISEASE

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