Using cases to strengthen inference on the association between single nucleotide polymorphisms and a secondary phenotype in genome-wide association studies.

ABSTRACT: Case-control genome-wide association studies provide a vast amount of genetic information that may be used to investigate secondary phenotypes. We study the situation in which the primary disease is rare and the secondary phenotype and genetic markers are dichotomous. An analysis of the association between a genetic marker and the secondary phenotype based on controls only (CO) is valid, whereas standard methods that also use cases result in biased estimates and highly inflated type I error if there is an interaction between the secondary phenotype and the genetic marker on the risk of the primary disease. Here we present an adaptively weighted (AW) method that combines the case and control data to study the association, while reducing to the CO analysis if there is strong evidence of an i

SUBMITTER: Li H 

PROVIDER: S-EPMC2918520 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature