Inferring Causal Phenotype Networks from Segregating Populations

A major goal in the study of complex traits is to decipher the causal interrelationships among correlated phenotypes. Current methods mostly yield undirected networks that connect phenotypes without causal orientation. Some of these connections may be spurious due to partial correlation that is not causal. We show how to build causal direction into an undirected network of phenotypes by including causal QTLs for each phenotype. We evaluate causal direction for each edge connecting two phenotypes using a LOD score. This new approach can be applied to many different population structures, including inbred and outbred crosses as well as natural populations, and can accommodate feedback loops. We assess its performance in simulation studies and show that our method recovers network edges and infers causal direction correctly at a high rate. Finally, we illustrate our method with an example involving gene expression and metabolite traits from experimental crosses.

Key Words: QTL, causal network, directed graph, eQTL, metabolomic QTL

Online ISS 1091-6490
Copyright 2008 by the Genetics Society of America
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