Nature Genetics
- 38, 1298 - 1303 (2006)
Published online: 22 October 2006; | doi:10.1038/ng1899
Transferability of tag SNPs in genetic association studies in multiple populationsPaul I W de Bakker1, 2, 3, 4, 16, Noël P Burtt1, 16, Robert R Graham1, 2, 3, 4, 16, Candace Guiducci1, Roman Yelensky1, 2, 3, 5, Jared A Drake1, 6, Todd Bersaglieri1, 6, Kathryn L Penney7, Johannah Butler1, 6, Stanton Young2, 3, Robert C Onofrio1, Helen N Lyon1, 6, Daniel O Stram8, Christopher A Haiman8, Matthew L Freedman1, 9, Xiaofeng Zhu10, Richard Cooper10, Leif Groop11, 12, Laurence N Kolonel13, Brian E Henderson8, Mark J Daly1, 2, 14, Joel N Hirschhorn1, 4, 6 & David Altshuler1, 2, 3, 4, 14, 151
Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts, 02142, USA. 2
Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114-2790, USA. 3
Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114-2790, USA. 4
Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. 5
Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA. 6
Divisions of Endocrinology and Genetics, Program in Genomics, Children's Hospital, Boston, Massachusetts 02115, USA. 7
Harvard School of Public Health, Boston, Massachusetts 02115, USA. 8
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA. 9
Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. 10
Department of Preventive Medicine and Epidemiology, Loyola University, Maywood, Illinois 60153, USA. 11
Department of Clinical Sciences, University Hospital, Lund University, Malmö S-20502, Sweden. 12
Department of Medicine, Helsinki University, Helsinki, Finland. 13
Cancer Research Center, University of Hawaii, Honolulu, Hawaii 96813, USA. 14
Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA. 15
Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. 16
These authors contributed equally to this work.
Correspondence should be addressed to David Altshuler altshuler@molbio.mgh.harvard.edu A general question for linkage disequilibrium–based association studies is how power to detect an association is compromised when tag SNPs are chosen from data in one population sample and then deployed in another sample. Specifically, it is important to know how well tags picked from the HapMap DNA samples capture the variation in other samples. To address this, we collected dense data uniformly across the four HapMap population samples and eleven other population samples. We picked tag SNPs using genotype data we collected in the HapMap samples and then evaluated the effective coverage of these tags in comparison to the entire set of common variants observed in the other samples. We simulated case-control association studies in the non-HapMap samples under a disease model of modest risk, and we observed little loss in power. These results demonstrate that the HapMap DNA samples can be used to select tags for genome-wide association studies in many samples around the world.
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