Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal-component analysis versus multidimensional scaling.

ABSTRACT: 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.

SUBMITTER: Wang D 

PROVIDER: S-EPMC2795880 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature