Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

Abstract

We undertook a meta-analysis of six Crohn's disease genome-wide association studies (GWAS) comprising 6,333 affected individuals (cases) and 15,056 controls and followed up the top association signals in 15,694 cases, 14,026 controls and 414 parent-offspring trios. We identified 30 new susceptibility loci meeting genome-wide significance (P < 5 × 10⁻⁸). A series of in silico analyses highlighted particular genes within these loci and, together with manual curation, implicated functionally interesting candidate genes including SMAD3, ERAP2, IL10, IL2RA, TYK2, FUT2, DNMT3A, DENND1B, BACH2 and TAGAP. Combined with previously confirmed loci, these results identify 71 distinct loci with genome-wide significant evidence for association with Crohn's disease.

Figure 1. Gene Relationships Across Implicated Loci (GRAIL) pathway analysis

Links between genes at 23 of 71 Crohn’s disease associated loci which scored P<0.01 using GRAIL. Specifically, of the 71 CD-associated SNPs, 69 are in LD intervals containing or within 50 kb of at least one gene. In total, there are 355 genes implicated by proximity to these 69 SNPs. Each observed CD-association was scored with GRAIL, which takes all genes mapping within CD-associated intervals and evaluates for each whether it is non-randomly linked to the other genes, via word-usage in PubMed abstracts. 23 SNPs shown in the outer circle are P<0.01 hits - indicating that the regions which they tag contain genes which are more significantly linked to genes in the other 68 regions than expected by chance at that level. The lines between genes represent individually significant connections that contribute to the positive signal, with thickness of lines inversely proportional to the probability a literature-based connection would be seen by chance. To accurately assess the statistical significance of this set of connections, we conducted simulations where we selected 1000 sets of 69 SNPs implicating in total 355 genes ±18 (5%) (selecting the SNPs randomly and using rejection sampling - only taking lists that implicated the same number of genes). Each of those 1000 sets were scored with GRAIL. The mean number of P<0.01 hits in a simulated list was 0.91 with a range in the 1000 sets from 0 to 11, suggesting that the likelihood of observing 23 hits with P<0.01 is far less than 0.1%.

Figure 2. Cumulative fraction of genetic variance explained by 71 CD loci

Cumulative fraction of genetic variance explained by the 71 CD loci reported here, ordered from largest to smallest individual contribution. Black points were identified pre-GWAS, green in first generation GWAS, blue in an earlier meta-analysis and cyan in this analysis. Inset shows a logarithmic fit to these data extrapolated to an extreme scenario where 20,000 independent common alleles are associated with disease. Even in this situation less than half of the genetic variance would be explained. This demonstrates that other types of effect (e.g. less common and rare alleles with higher penetrance) must also exist.