Model-based clustering for identifying disease-associated SNPs in case-control genome-wide association studies

TL;DR

This paper introduces a model-based clustering method for GWAS data that improves detection of disease-associated SNPs by leveraging information across SNPs and controlling false discovery rates more effectively.

Contribution

The authors propose a novel clustering approach that transforms high-dimensional GWAS analysis into a more manageable form, outperforming traditional methods in simulations and real data analysis.

Findings

Better control of false discovery rate (FDR) in simulations

Detection of known and novel SNPs in real GWAS data

Outperforms traditional SNP-wise approach in sensitivity

Abstract

Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing adjustment is over-conservative and lack of power in many GWASs. In this article, we proposed a model-based clustering method that transforms the challenging high-dimension-small-sample-size problem to low-dimension-large-sample-size problem and borrows information across SNPs by grouping SNPs into three clusters. We pre-specify the patterns of clusters by minor allele frequencies of SNPs between cases and controls, and enforce the patterns with prior distributions. In the simulation studies our proposed novel model outperform traditional SNP-wise approach by showing better controls of false discovery rate (FDR) and higher sensitivity. We re-analyzed two real studies to identifying SNPs associated with severe bortezomib-induced peripheral neuropathy (BiPN) in patients with multiple myeloma (MM). The original analysis in the literature failed to identify SNPs after FDR adjustment. Our proposed method not only detected the reported SNPs after FDR adjustment but also discovered a novel BiPN-associated SNP rs4351714 that has been reported to be related to MM in another study.