A multiple coefficient of determination-based method for parsing SNPs that correlate with mRNA expression.

ABSTRACT: In this study, we present a novel, multiple coefficient of determination (R²_M)-based method for parsing SNPs located within the chromosomal neighborhood of a gene into semi-independent families, each of which corresponds to one or more functional variants that regulate transcription of the gene. Specifically, our method utilizes a matrix equation framework to calculate R²_M values for SNPs within a chromosome region of interest (ROI) based upon the choices of 1-4 "index" SNPs (iSNPs) that serve as proxies for underlying regulatory variants. Exhaustive testing of sets of 1-4 candidate iSNPs identifies iSNP models that best account for estimated R² values derived from single-variable linear regression analysis of correlations between mRNA

SUBMITTER: Song F 

PROVIDER: S-EPMC6934451 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature