Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes

Genetic variation can modulate response to treatment (G×T) or environmental stimuli (G×E), both of which may be highly consequential in biomedicine. An effective approach to identifying G×T signals and gaining insight into molecular mechanisms is mapping quantitative trait loci (QTL) of molecular count phenotypes, such as gene expression and chromatin accessibility, under multiple treatment conditions, which is termed response molecular QTL mapping. Although standard approaches evaluate the interaction between genetics and treatment conditions, they do not distinguish between meaningful interpretations such as whether a genetic effect is only observed in the treated condition or whether a genetic effect is observed but accentuated in the treated condition. To address this gap, we have developed a downstream method for classifying response molecular QTLs into subclasses with meaningful genetic interpretations. Our method uses Bayesian model selection and assigns posterior probabilities to different types of G×T interactions for a given feature-SNP pair. We compare linear and nonlinear regression of log-scale counts, noting that the latter accounts for an expected biological relationship between the genotype and the molecular count phenotype. Through simulation and application to existing datasets of molecular response QTLs, we show that our method provides an intuitive and well-powered framework to report and interpret G×T interactions. We provide a software package, ClassifyGxT, which is available at https://github.com/yharigaya/classifygxt.