Copyright ©2009 The WJG Press and Baishideng. All rights reserved.
World J Gastroenterol. Nov 21, 2009; 15(43): 5377-5396
Published online Nov 21, 2009. doi: 10.3748/wjg.15.5377
Genome-wide association studies - A summary for the clinical gastroenterologist
Espen Melum, Andre Franke, Tom H Karlsen
Espen Melum, Tom H Karlsen, Medical Department, Rikshospitalet, Oslo University Hospital, N-0027 Oslo, Norway; Research Institute for Internal Medicine, Rikshospitalet, Oslo University Hospital, N-0027 Oslo, Norway
Andre Franke, Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany
Author contributions: Melum E searched the literature for relevant articles; Melum E and Karlsen TH wrote the paper; Franke A critically evaluated and edited the manuscript; All authors approved the final manuscript.
Correspondence to: Tom H Karlsen, MD, PhD, Norwegian PSC research center, Medical Department, Rikshospitalet, Oslo University Hospital, Sognsvannsvn. 20, N-0027 Oslo, Norway. t.h.karlsen@medisin.uio.no
Telephone: +47-23072469  Fax: +47-23074869
Received: September 1, 2009
Revised: September 16, 2009
Accepted: September 23, 2009
Published online: November 21, 2009

Genome-wide association studies (GWAS) have been applied to various gastrointestinal and liver diseases in recent years. A large number of susceptibility genes and key biological pathways in disease development have been identified. So far, studies in inflammatory bowel diseases, and in particular Crohn’s disease, have been especially successful in defining new susceptibility loci using the GWAS design. The identification of associations related to autophagy as well as several genes involved in immunological response will be important to future research on Crohn’s disease. In this review, key methodological aspects of GWAS, the importance of proper cohort collection, genotyping issues and statistical methods are summarized. Ways of addressing the shortcomings of the GWAS design, when it comes to rare variants, are also discussed. For each of the relevant conditions, findings from the various GWAS are summarized with a focus on the affected biological systems.

Keywords: Genome-wide association studies, Inflammatory bowel disease, Gastroenterology, Hepatology