Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain
Deciphering the environmental contexts at which genetic effects are most prominent is central for making full use of GWAS results in follow-up experiment design and treatment development. However, measuring a large number of environmental factors at high granularity might not always be feasible. Instead, here we propose extracting cellular embedding of environmental factors from gene expression data by using latent variable (LV) analysis and taking these LVs as environmental proxies in detecting gene-by-environment (GxE) interaction effects on gene expression, i.e., GxE expression quantitative trait loci (eQTLs).
Source: The American Journal of Human Genetics - Category: Genetics & Stem Cells Authors: Bernard Ng, William Casazza, Ellis Patrick, Shinya Tasaki, Gherman Novakovsky, Daniel Felsky, Yiyi Ma, David A. Bennett, Chris Gaiteri, Philip L. De Jager, Sara Mostafavi Tags: Article Source Type: research