Supervised categorical principal component analysis for genome-wide association analyses.

In order to have a better understanding of unexplained heritability for complex diseases in conventional Genome-Wide Association Studies (GWAS), aggregated association analyses based on predefined functional regions, such as genes and pathways, become popular recently as they enable evaluating joint effect of multiple Single-Nucleotide Polymorphisms (SNPs), which helps increase the detection power, especially when investigating genetic variants with weak individual effects. In this paper, we focus on aggregated analysis methods based on the idea of Principal Component Analysis (PCA). The past approaches using PCA mostly make some inherent genotype data and/or risk effect model assumptions, which may hinder the accurate detection of potential disease SNPs that influence disease phenotypes. In this paper, we derive a general Supervised Categorical Principal Component Analysis (SCPCA), which explicitly models categorical SNP data without imposing any risk effect model assumption. We have evaluated the efficacy of SCPCA with the comparison to a traditional Supervised PCA (SPCA) and a previously developed Supervised Logistic Principal Component Analysis (SLPCA) based on both the simulated genotype data by HAPGEN2 and the genotype data of Crohn's Disease (CD) from Wellcome Trust Case Control Consortium (WTCCC). Our preliminary results have demonstrated the superiority of SCPCA over both SPCA and SLPCA due to its modeling explicitly designed for categorical SNP data as well as its flexibility on the risk effect model assumption.