Uncovering rare genetic variants predisposing to coeliac disease

Abstract

Coeliac disease is a common (1% prevalence) inflammatory disease of the small intestine, involving the role of tissue transglutaminase and HLA-­‐DQ binding immuno-­‐dominant wheat peptides. The disease is highly heritable, however, at most only 40% of this heritability is explained by HLA-­‐DQ and risk variants from genome wide association and fine mapping studies. The hypothesis of the research in this thesis is that rare (minor allele frequency <0.5%) mutations of large effect size (odds ratios ~2 – 5) exist, especially in multiply affected pedigrees, which account for the missing heritability of disease. NimbleGen exome capture and Illumina GAIIx high throughput sequencing was performed in 75 coeliac disease individuals from 55 multiply affected families. Candidate genes were chosen from various analytical strategies: linkage, shared variants between multiple related subjects and gene burden tests for multiple potentially causal variants. Highly multiplexed amplicon sequencing, using Fluidigm technology, of all RefSeq exons from 24 candidate genes in 2,304 coeliac cases and 2,304 controls was performed to locate further rare variation. Gene burden tests on a highly stringent post quality control dataset identified no significant associations (P<1x10-­‐3) at the resequenced candidate genes. The strategy of sequencing multiply affected families, and deep follow up of candidate genes, has not identified new disease risk mutations. Common variants (and other factors, e.g. environmental) may instead account for familial clustering in this common autoimmune disease