Research ArticleExtended analysis of a genome-wide association study in primary sclerosing cholangitis detects multiple novel risk loci
Introduction
Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown etiology, characterized by progressive inflammation and fibrosis of the bile ducts, leading to liver cirrhosis in many cases [1]. An important clinical feature of PSC is the frequent autoimmune manifestations in other organ systems, most commonly inflammatory bowel disease (IBD), which is reported in 62–83% of PSC patients of Northern European descent [1]. In addition, approximately 25% of PSC patients are affected with at least one autoimmune disease outside the liver and colon [2], most commonly, type 1 diabetes, thyroid disease, rheumatoid arthritis and psoriasis. Shared genetic susceptibility could potentially explain the frequent occurrence of these immune-related co-morbidities in PSC.
The importance of genetic risk factors in PSC is demonstrated by heritability studies estimating siblings of PSC patients to be 9–39 times more likely to develop PSC than the general population [1]. The contribution of genetic variants in the HLA complex on chromosome 6p21 to the risk of PSC is well established [1]. Previously, strong evidence for associated risk factors outside the HLA region has been reported at chromosome 3p21 in MST1 and chromosome 2q13 near BCL2L11 [3]. In addition, suggestive PSC associations have been reported at six additional loci harboring the likely susceptibility genes GPBAR1, IL2RA, GPC5/GPC6, IL2/IL21, CARD9, and REL [3], [4], [5], [6]. In the most recent PSC GWAS [3], only the top 23 associated regions were selected for replication genotyping.
Replication attempts of promising, but lower ranked markers from GWAS have yielded valuable findings in several other diseases, and have been particularly fruitful when combined with a semi-hypothesis-driven approach taking into consideration gene content and potential biological relevance [7]. In an attempt to identify novel susceptibility loci in PSC, we selected a second tier of promising associated markers from an available PSC GWAS [3] for replication in an independent cohort.
Section snippets
Study subjects
The discovery panel included a total of 715 PSC cases and 2962 healthy controls, with 332 PSC cases and 262 controls from Scandinavia, and 383 PSC cases and 2700 controls from Germany [3]. The replication panel consisted of a total of 1221 PSC cases and 3508 controls, with 289 PSC cases and 820 controls from Scandinavia, 561 PSC patients and 2063 controls from Central Europe, and 371 PSC cases and 625 controls from the United States (US).
The recruitment of study subjects is described in detail
SNP selection and genotyping results
Seven hundred and fifteen PSC patients and 2962 controls were successfully genotyped and analyzed in the GWAS (Table 1). Among the 2,466,182 genotyped and imputed SNPs analyzed, a subset of 59 SNPs were selected for follow-up; 37 SNPs based on SNP selection strategy I and 22 SNPs based on SNP selection strategy II. Following quality pruning of the replication dataset, a total of 45 SNPs were included in the association analysis.
Association results
A total of 17 SNPs achieved nominal significance in the replication
Discussion
In the largest PSC cohort presented, we performed replication genotyping and a combined analysis of 45 SNPs not followed up in a previous GWAS in PSC [3]. We identified one novel PSC risk locus with association results below the threshold for genome-wide significance along with suggestive evidence for replication of 8 novel additional loci. The PSC-associated FUT2 variant was shown to significantly influence the bile microbial community composition in PSC patients.
The replicated SNP at 1p36 (
Financial support
The study was supported by The Norwegian PSC Research Center (http://ous-research.no/nopsc/) and the German Ministry of Education and Research (BMBF) through the National Genome Research Network (NGFN) and the Integrated Research and Treatment Center – Transplantation (reference number: 01EO0802) and the PopGen biobank (http://www.popgen.de). The US part of the study was supported by the NIH (DK 84960). The project received infrastructure support through the Norwegian Functional Genomics
Conflict of interest
The authors who have taken part in this study declared that they do not have anything to disclose regarding funding or conflict of interest with respect to this manuscript.
Acknowledgements
The authors are indebted to all PSC patients and healthy controls for their participation. We thank Katja Cloppenborg-Schmidt, Ilona Urbach, Irene Pauselis, Tanja Wesse, Tanja Henke, Rainer Vogler, Hege Dahlen Sollid, Bente Woldseth, and Liv Wenche Torbjørnsen for expert technical help. Paul R. Berg and Silje Karoliussen are specially thanked for providing expert assistance in the genotyping process. We are grateful to Arthur Kaser and Michael Nothnagel for helpful discussions. Benedicte A. Lie
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These authors contributed equally to this work.