Open AccessA Rapid Association Test Procedure Robust under Different Genetic Models Accounting for Population Stratification
Author(s) -
Wenan Chen,
Xiangning Chen,
Kellie J. Archer,
Nianjun Liu,
Qizhai Li,
Zhongming Zhao,
Shumei S. Sun,
Guimin Gao
Publication year - 2013
Publication title -
human heredity
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.423
H-Index - 62
eISSN - 1423-0062
pISSN - 0001-5652
DOI - 10.1159/000350109
Subject(s) - population stratification , genetic association , genome wide association study , population , statistics , linkage disequilibrium , additive model , econometrics , mathematics , computer science , biology , medicine , genetics , allele , genotype , single nucleotide polymorphism , environmental health , gene , haplotype
For genome-wide association studies (GWAS) using case-control data with stratification, a commonly used association test is the generalized Armitage (GA) trend test implemented in the software EIGENSTRAT. The GA trend test uses principal component analysis to correct for population stratification. It usually assumes an additive disease model and can have high power when the underlying disease model is additive or multiplicative, but may have relatively low power when the underlying disease model is recessive or dominant. The purpose of this paper is to provide a test procedure for GWAS with increased power over the GA trend test under the recessive and dominant models, while maintaining the power of the GA trend test under the additive and multiplicative models.