Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes

Natalie J Prescott, Benjamin Lehne, Kristina Stone, James C Lee, Kirstin Taylor, Jo Knight, Efterpi Papouli, Muddassar M Mirza, Michael A Simpson, Sarah L Spain, Grace Lu, Franca Fraternali, Suzannah J Bumpstead, Emma Gray, Ariella Amar, Hannah Bye, Peter Green, Guy Chung-Faye, Bu'Hussain Hayee, Richard PollokJack Satsangi, Miles Parkes, Jeffrey C Barrett, John C Mansfield, Jeremy Sanderson, Cathryn M Lewis, Michael E Weale, Thomas Schlitt, Christopher G Mathew, UK IBD Genetics Consortium, Paul Henderson (Member of Consortium)

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.
Original languageEnglish
Article numbere1004955
Number of pages19
JournalPLoS Genetics
Issue number2
Publication statusPublished - 11 Feb 2015

Keywords / Materials (for Non-textual outputs)

  • Colitis, Ulcerative
  • Crohn Disease
  • Genetic Association Studies
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study
  • HLA Antigens
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Membrane Glycoproteins
  • Phenotype
  • Polymorphism, Single Nucleotide


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