The purpose of this technical report is to describe a novel method developed to detect association between a genetic marker and multiple phenotypes. In order to obtain a one-degree of freedom test, a generalized principal component approach is suggested that aggregates the information about the genetic effect in the ﬁrst prin- cipal component, while the remain principal components contain only environment noise. A limited simulation study is done validating the method. For scenarios in which the genetic effect is constant across all measurements and there is no envi- ronmental correlation between the measurements, preliminary results suggest that this method has similar power to standard methods of analysis. Since such setups favor the standard approach, the new method is expected to be efﬁcient for many realistic alternative hypotheses, including those with varying genetic effect sizes across measurements and those accounting for environmental correlation.
Naylor, Melissa and Lange, Christoph, "C2BAT: A Novel Method for Association Between Ge- netic Markers and Multiple Phenotypes" (February 2012). Harvard University Biostatistics Working Paper Series. Working Paper 147.