Block-based Bayesian epistasis association mapping with application to WTCCC type 1 diabetes data

TL;DR

This paper introduces a Bayesian approach for identifying gene interactions in genome-wide SNP data, effectively partitioning SNPs into LD-blocks and detecting disease associations, demonstrated on type 1 diabetes data.

Contribution

A novel Bayesian method for partitioning SNPs into LD-blocks and identifying associated SNPs, improving detection of multi-locus interactions in genome-wide data.

Findings

Accurate LD-block partitioning with measures of uncertainty

Enhanced power to detect multi-locus associations

Identification of known T1D genes in WTCCC data

Abstract

Interactions among multiple genes across the genome may contribute to the risks of many complex human diseases. Whole-genome single nucleotide polymorphisms (SNPs) data collected for many thousands of SNP markers from thousands of individuals under the case--control design promise to shed light on our understanding of such interactions. However, nearby SNPs are highly correlated due to linkage disequilibrium (LD) and the number of possible interactions is too large for exhaustive evaluation. We propose a novel Bayesian method for simultaneously partitioning SNPs into LD-blocks and selecting SNPs within blocks that are associated with the disease, either individually or interactively with other SNPs. When applied to homogeneous population data, the method gives posterior probabilities for LD-block boundaries, which not only result in accurate block partitions of SNPs, but also provide measures of partition uncertainty. When applied to case--control data for association mapping, the method implicitly filters out SNP associations created merely by LD with disease loci within the same blocks. Simulation study showed that this approach is more powerful in detecting multi-locus associations than other methods we tested, including one of ours. When applied to the WTCCC type 1 diabetes data, the method identified many previously known T1D associated genes, including PTPN22, CTLA4, MHC, and IL2RA.