publication . Article . Other literature type . 2009

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

Wang, Dai; Sun, Yu; Stang, Paul; Berlin, Jesse A; Wilcox, Marsha A; Li, Qingqin;
Open Access
  • Published: 01 Dec 2009 Journal: BMC Proceedings, volume 3 (eissn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
Abstract
<p>Abstract</p> <p>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 associat...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Genetic association, Genetic analysis, Genome-wide association study, Bioinformatics, Rheumatoid arthritis, medicine.disease, medicine, Principal component analysis, business.industry, business, Multidimensional scaling, Population stratification, Population, education.field_of_study, education, R, Science, Q, Proceedings
Funded by
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

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