Identifying causal genotype-phenotype relationships for population-sampled parent-child trios

The process by which genes are transmitted from parent to child provides a source of randomization preceding all other factors that may causally influence any particular child phenotype. Because of this, it is natural to consider genetic transmission as a source of experimental randomization. In this work, we show how parent-child trio data can be leveraged to identify causal genetic loci by modeling the randomization during genetic transmission. We develop a new test, the transmission mean test (TMT), together with its unbiased estimator of the average causal effect, and derive its causal properties within the potential outcomes framework. We also prove that the transmission disequilibrium test (TDT) is a test of causality as a complementary case of the TMT for the affected-only design. The TMT and the TDT differ in the types of traits that they can handle and the study designs for which they are appropriate. The TMT handles arbitrarily distributed traits and is appropriate when trios are randomly sampled; the TDT handles dichotomous traits and is appropriate when sampling is based on a child's trait status. We compare the transmission-based methods with established approaches for genotype-phenotype analyses to clarify conditions appropriate for each method, what conclusions can be drawn by each one, and how these methods can be used together.