Model-based clustering for identifying disease-associated SNPs in case-control genome-wide association studies
This method addresses the challenge of identifying disease-associated SNPs in GWASs for researchers in genetics and medicine, offering improved detection power over traditional methods, though it is incremental as it builds on existing clustering and prior distribution techniques.
The authors tackled the problem of low power in genome-wide association studies (GWASs) by proposing a model-based clustering method that groups SNPs into three clusters based on allele frequency patterns, which outperformed traditional approaches in simulations with better false discovery rate control and higher sensitivity, and in real data re-analysis, it detected previously reported SNPs and a novel SNP associated with severe bortezomib-induced peripheral neuropathy.
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.