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1 Division of General Internal Medicine, Departments of 2 Medicine and 3 Biopharmaceutical Sciences, 4 Center for Human Genetics, and 5 Comprehensive Cancer Center, University of California San Francisco, San Francisco, California and 6 Northern California Cancer Center, Fremont, California
Requests for reprints: Elad Ziv, Division of General Internal Medicine, University of California San Francisco, Box 1732, San Francisco, CA 94143. Phone: 415-353-7981; Fax: 415-353-7932. E-mail: elad.ziv{at}ucsf.edu
Background: Genetic association studies using case-control designs are susceptible to false-positive and false-negative results if there are differences in genetic ancestry between cases and controls. We measured genetic ancestry among Latinas in a population-based case-control study of breast cancer and tested the association between ancestry and known breast cancer risk factors. We reasoned that if genetic ancestry is associated with known breast cancer risk factors, then the results of genetic association studies would be confounded.
Methods: We used 44 ancestry informative markers to estimate individuals' genetic ancestry in 563 Latina participants. To test whether ancestry is a predictor of hormone therapy use, parity, and body mass index (BMI), we used multivariate logistic regression models to estimate odds ratios (OR) and 95% confidence intervals (95% CI) associated with a 25% increase in Indigenous American ancestry, adjusting for age, education, and the participant's and grandparents' place of birth.
Results: Hormone therapy use was significantly less common among women with higher Indigenous American ancestry (OR, 0.78; 95% CI, 0.63-0.96). Higher Indigenous American ancestry was also significantly associated with overweight (BMI, 25-29.9 versus <25) and obesity (BMI, 
30 versus <25), but only among foreign-born Latina women (OR, 3.44; 95% CI, 1.97-5.99 and OR, 1.95; 95% CI, 1.24-3.06, respectively).
Conclusion: Some breast cancer risk factors are associated with genetic ancestry among Latinas in the San Francisco Bay Area. Therefore, case-control genetic association studies for breast cancer should directly measure genetic ancestry to avoid potential confounding. (Cancer Epidemiol Biomarkers Prev 2006;15(10):1878–85)
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