![Figure 1. Summary of strategy for detecting rare variants associated with IBD.
Overview of our rare variant screening strategy in IBD using DNA pools. We detected 3442 high quality variants in phase I based on stringent filtering criteria. We were able to validate 1252 of these variants using a) previously generated genotyping data for 153 SNPs in 634 of the individuals who were sequenced; b) case-control association p values for 1099 SNPs from CD Immunochip study [4]. We then performed validation genotyping of 80 variants in phase II in 6335 IBD cases and 2974 controls and extended the analysis of the top 5 SNVs to a further 3662 IBD cases and 3639 controls (phase III) to allow a final combined analysis of 10,147 IBD cases and 7,008 controls.](https://www.researchgate.net/profile/Thomas-Schlitt/publication/272190181/figure/fig3/AS:341286587518990@1458380472043/Summary-of-strategy-for-detecting-rare-variants-associated-with-IBD-Overview-of-our-rare_Q320.jpg)
![Figure 2. Minor allele frequencies WTCCC vs pooled NGS (24 pools combined).
MAFs for 153 SNPs were compared between allele frequency estimates based on pooled NGS and genotyping data from the WTCCC [47] for 634 individuals. MAFs are strongly correlated between both datasets (Spearman rank correlation coefficient R = 0.976), with only two SNPs showing substantial differences.](https://www.researchgate.net/profile/Thomas-Schlitt/publication/272190181/figure/fig4/AS:341525788676108@1458437501752/Minor-allele-frequencies-WTCCC-vs-pooled-NGS-24-pools-combined-MAFs-for-153-SNPs-were_Q320.jpg)
February 2015
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56 Citations
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.
