Pooled sequencing of 531 genes in inflammatory bowel disease identifies an associated rare variant in BTNL2 and implicates other immune related genes

• Published in: PLoS genetics 2015-02, Vol.11 (2), p.e1004955-e1004955
• Main Authors: Prescott, Natalie J, Lehne, Benjamin, Stone, Kristina, Lee, James C, Taylor, Kirstin, Knight, Jo, Papouli, Efterpi, Mirza, Muddassar M, Simpson, Michael A, Spain, Sarah L, Lu, Grace, Fraternali, Franca, Bumpstead, Suzannah J, Gray, Emma, Amar, Ariella, Bye, Hannah, Green, Peter, Chung-Faye, Guy, Hayee, Bu'Hussain, Pollok, Richard, Satsangi, Jack, Parkes, Miles, Barrett, Jeffrey C, Mansfield, John C, Sanderson, Jeremy, Lewis, Cathryn M, Weale, Michael E, Schlitt, Thomas, Mathew, Christopher G
• Format: Article
• Language: English
• Subjects: Butyrophilins; Colitis, Ulcerative - genetics; Colitis, Ulcerative - immunology; Colitis, Ulcerative - pathology; Crohn Disease - genetics; Crohn Disease - immunology; Crohn Disease - pathology; DNA sequencing; Genes; Genetic aspects; Genetic Association Studies; Genetic Predisposition to Disease; Genetic variation; Genome-Wide Association Study; High-Throughput Nucleotide Sequencing; HLA Antigens - genetics; Humans; Identification and classification; Inflammatory bowel disease; Inflammatory bowel diseases; Medical research; Membrane Glycoproteins - genetics; Methods; Phenotype; Polymorphism, Single Nucleotide; Studies
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1004955

The contribution of rare coding sequence variants to genetic susceptibility in complex disorders is an important but unresolved question. Most studies thus far have investigated a limited number of genes from regions which contain common disease associated variants. Here we investigate this in inflammatory bowel disease by sequencing the exons and proximal promoters of 531 genes selected from both genome-wide association studies and pathway analysis in pooled DNA panels from 474 cases of Crohn's disease and 480 controls. 80 variants with evidence of association in the sequencing experiment or with potential functional significance were selected for follow up genotyping in 6,507 IBD cases and 3,064 population controls. The top 5 disease associated variants were genotyped in an extension panel of 3,662 IBD cases and 3,639 controls, and tested for association in a combined analysis of 10,147 IBD cases and 7,008 controls. A rare coding variant p.G454C in the BTNL2 gene within the major histocompatibility complex was significantly associated with increased risk for IBD (p = 9.65x10-10, OR = 2.3[95% CI = 1.75-3.04]), but was independent of the known common associated CD and UC variants at this locus. Rare (