Generalized Analysis of Molecular variance for Mixed model Analysis (GAMMA)
A typical GWAS tests correlation between a single phenotype and each genotype one at a time. However, it is often very useful to analyze many phenotypes simultaneously. For example, this may increase the power to detect variants by capturing unmeasured aspects of complex biological networks that a single phenotype might miss. There are several multivariate approaches that try to detect variants related to many phenotypes, but none of them consider population structure and each may result in a significant number of false positive identifications. Here, we introduce a new methodology, referred to as GAMMA, that could both simultaneously analyze many phenotypes as well as correct for population structure. In a simulated study, GAMMA accurately identifies true genetic effects without false positive identifications, while other methods either fail to detect true effects or result in many false positive identifications. We further apply our method to genetic studies of yeast and gut microbiome from mouse and show that GAMMA identifies several variants that are likely to have a true biological mechanism.
The R implementation of GAMMA is available. Please refer to the Documentation link for further information. If you have you any further question, please contact Jong Wha J Joo. This is the joint work with Eun yong Kand, Elin Org, Nick Furlotte, Brian Parks, Aldons J. Lusis and Eleazar Eskin.
This web-site is based upon work supported by the National Science Foundation under Grant No. 0513599 and 0729049. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.