Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal-component analysis versus multidimensional scaling.
Population stratification (PS) represents a major challenge in genome-wide association studies. Using the Genetic Analysis Workshop 16 Problem 1 data, which include samples of rheumatoid arthritis patients and healthy controls, we compared two methods that can be used to evaluate population structure and correct PS in genome-wide association studies: the principal-component analysis method and the multidimensional-scaling method. While both methods identified similar population structures in this dataset, principal-component analysis performed slightly better than the multidimensional-scaling method in correcting for PS in genome-wide association analysis of this dataset.
Wang
Dai
D
Department of Pharmacogenomics, Johnson & Johnson Pharmaceutical Research and Development, LLC, Raritan, New Jersey 08869 USA. dwang39@its.jnj.com.
Sun
Yu
Y
Stang
Paul
P
Berlin
Jesse A
JA
Wilcox
Marsha A
MA
Li
Qingqin
Q