Rights statement: © 2015 Prescott et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
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Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
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TY - JOUR
T1 - Pooled sequencing of 531 genes in inflammatory bowel disease identifies an associated rare variant in BTNL2 and implicates other immune related genes
AU - Prescott, Natalie J.
AU - Lehne, Benjamin
AU - Stone, Kristina
AU - Lee, James C.
AU - Taylor, Kirstin
AU - Knight, Jo
AU - Papouli, Efterpi
AU - Mirza, Muddassar M.
AU - Simpson, Michael A.
AU - Spain, Sarah L.
AU - Lu, Grace
AU - Fraternali, Franca
AU - Bumpstead, Suzannah J.
AU - Gray, Emma
AU - Amar, Ariella
AU - Bye, Hannah
AU - Green, Peter
AU - Chung-Faye, Guy
AU - Hayee, Bu'Hussain
AU - Pollok, Richard
AU - Satsangi, Jack
AU - Parkes, Miles
AU - Barrett, Jeffrey C.
AU - Mansfield, John C.
AU - Sanderson, Jeremy
AU - Lewis, Cathryn M.
AU - Weale, Michael E.
AU - Schlitt, Thomas
AU - Mathew, Christopher G.
AU - UK IBD Genetics Consortium
N1 - © 2015 Prescott et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
PY - 2015/2/11
Y1 - 2015/2/11
N2 - 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 (<1%) and low frequency (1-5%) variants in 3 additional genes showed suggestive association (p<0.005) with either an increased risk (ARIH2 c.338-6C>T) or decreased risk (IL12B p.V298F, and NICN p.H191R) of IBD. These results provide additional insights into the involvement of the inhibition of T cell activation in the development of both sub-phenotypes of inflammatory bowel disease. We suggest that although rare coding variants may make a modest overall contribution to complex disease susceptibility, they can inform our understanding of the molecular pathways that contribute to pathogenesis.
AB - 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 (<1%) and low frequency (1-5%) variants in 3 additional genes showed suggestive association (p<0.005) with either an increased risk (ARIH2 c.338-6C>T) or decreased risk (IL12B p.V298F, and NICN p.H191R) of IBD. These results provide additional insights into the involvement of the inhibition of T cell activation in the development of both sub-phenotypes of inflammatory bowel disease. We suggest that although rare coding variants may make a modest overall contribution to complex disease susceptibility, they can inform our understanding of the molecular pathways that contribute to pathogenesis.
KW - Colitis, Ulcerative
KW - Crohn Disease
KW - Genetic Association Studies
KW - Genetic Predisposition to Disease
KW - Genome-Wide Association Study
KW - HLA Antigens
KW - High-Throughput Nucleotide Sequencing
KW - Humans
KW - Membrane Glycoproteins
KW - Phenotype
KW - Polymorphism, Single Nucleotide
U2 - 10.1371/journal.pgen.1004955
DO - 10.1371/journal.pgen.1004955
M3 - Journal article
C2 - 25671699
VL - 11
JO - PLoS Genetics
JF - PLoS Genetics
SN - 1553-7390
IS - 2
M1 - e1004955
ER -