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Transferability of tag SNPs in genetic association studies in multiple populations

de Bakker, Paul I. W. ; Burtt, Noel P. ; Graham, Robert R. ; Guiducci, Candace ; Yelensky, Roman ; Drake, Jared A. ; Bersaglieri, Todd ; Penney, Kathryn L. ; Butler, Johannah and Young, Stanton , et al. (2006) In Nature Genetics 38(11). p.1298-1303
Abstract
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... (More)
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. (Less)
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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nature Genetics
volume
38
issue
11
pages
1298 - 1303
publisher
Nature Publishing Group
external identifiers
  • wos:000241592700018
  • scopus:33750471977
ISSN
1546-1718
DOI
10.1038/ng1899
language
English
LU publication?
yes
id
40b917ed-e63f-4dbd-b67a-d3c5506d16e9 (old id 378665)
date added to LUP
2016-04-01 16:31:11
date last changed
2020-12-29 04:30:41
@article{40b917ed-e63f-4dbd-b67a-d3c5506d16e9,
  abstract     = {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.},
  author       = {de Bakker, Paul I. W. and Burtt, Noel P. and Graham, Robert R. and Guiducci, Candace and Yelensky, Roman and Drake, Jared A. and Bersaglieri, Todd and Penney, Kathryn L. and Butler, Johannah and Young, Stanton and Onofrio, Robert C. and Lyon, Helen N. and O Stram, Daniel and Haiman, Christopher A. and Freedman, Matthew L. and Zhu, Xiaofeng and Cooper, Richard and Groop, Leif and Kolonel, Laurence N. and Henderson, Brian E. and Daly, Mark J. and Hirschhorn, Joel N. and Altshuler, David},
  issn         = {1546-1718},
  language     = {eng},
  number       = {11},
  pages        = {1298--1303},
  publisher    = {Nature Publishing Group},
  series       = {Nature Genetics},
  title        = {Transferability of tag SNPs in genetic association studies in multiple populations},
  url          = {http://dx.doi.org/10.1038/ng1899},
  doi          = {10.1038/ng1899},
  volume       = {38},
  year         = {2006},
}