Examining Population Stratification via Individual Ancestry Estimates versus Self-Reported Race

Posted in Articles, Health/Medicine/Genetics, Latino Studies, Media Archive on 2011-12-09 04:43Z by Steven

Examining Population Stratification via Individual Ancestry Estimates versus Self-Reported Race

Cancer Epidemiology, Biomarkers & Prevention
Volume 14, Issue 6 (June 2005)
pages 1545-1551
DOI: 10.1158/1055-9965.EPI-04-0832

Jill S. Barnholtz-Sloan
Cancer Prevention and Control Program
H. Lee Moffitt Cancer Center and Research Institute

Ranajit Chakraborty
Center for Genome Research, Department of Environmental Health
University of Cincinnati, Cincinnati, Ohio

Thomas A. Sellers
Cancer Prevention and Control Program
H. Lee Moffitt Cancer Center and Research Institute

Ann G. Schwartz
Population Studies and Prevention Program, Karmanos Cancer Institute and Department of Internal Medicine
Wayne State University School of Medicine, Detroit, Michigan

Population stratification has the potential to affect the results of genetic marker studies. Estimating individual ancestry provides a continuous measure to assess population structure in case-control studies of complex disease, instead of using self-reported racial groups. We estimate individual ancestry using the Federal Bureau of Investigation CODIS Core short tandem repeat set of 13 loci using two different analysis methods in a case-control study of early-onset lung cancer. Individual ancestry proportions were estimated for “European” and “West African” groups using published allele frequencies. The majority of Caucasian, non-Hispanics had >50% European ancestry, whereas the majority of African Americans had <20% European ancestry, regardless of ancestry estimation method, although significant overlap by self-reported race and ancestry also existed. When we further investigated the effect of ancestry and self-reported race on the frequency of a lung cancer risk genotype, we found that the frequency of the GSTM1 null genotype varies by individual European ancestry and case-control status within self-reported race (particularly for African Americans). Genetic risk models showed that adjusting for individual European ancestry provided a better fit to the data compared with the model with no group adjustment or adjustment for self-reported race. This study suggests that significant population substructure differences exist that self-reported race alone does not capture and that individual ancestry may be confounded with disease status and/or a candidate gene risk genotype.

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