Generalized genetical genomics
It is argued that more comprehensive analysis and Bayesian reasoning are needed and can overcome some of these pitfalls, although not in every conceivable case.
Abstract
Genome-wide linkage and association studies of tens of thousands of clinical and molecular traits are currently under way, offering rich data for inferring causality between traits and genetic variation. However, the inference process is based on discovering subtle patterns in the correlation between traits and is therefore challenging and could create a flood of untrustworthy causal inferences. Here we introduce the concerns and show they are valid already in simple scenarios of two traits linked or associated to the same genomic region. We argue that more comprehensive analysis and Bayesian reasoning are needed and can overcome some of these pitfalls, although not in every conceivable case. We conclude that causal inference methods may still be of use in the iterative process of mathematical modeling and biological validation