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Discerning the ancestry of European Americans in genetic association studies

Price, Alkes L.; Butler, Johannah; Patterson, Nick; Capelli, Cristian; Pascali, Vincenzo L.; Scarnicci, Francesca; Ruiz-Linares, Andres; Groop, Leif LU ; Saetta, Angelica A. and Korkolopoulou, Penelope, et al. (2008) In PLoS Genetics 4(1).
Abstract
European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false-positive or false-negative associations due to population stratification and to identify genetic variants whose contribution to disease risk differs across European ancestries. Here, we investigate empirical patterns of population structure in European Americans, analyzing 4,198 samples from four genome-wide association studies to show that components roughly corresponding to northwest European, southeast European, and Ashkenazi Jewish ancestry are the main... (More)
European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false-positive or false-negative associations due to population stratification and to identify genetic variants whose contribution to disease risk differs across European ancestries. Here, we investigate empirical patterns of population structure in European Americans, analyzing 4,198 samples from four genome-wide association studies to show that components roughly corresponding to northwest European, southeast European, and Ashkenazi Jewish ancestry are the main sources of European American population structure. Building on this insight, we constructed a panel of 300 validated markers that are highly informative for distinguishing these ancestries. We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data. (Less)
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PLoS Genetics
volume
4
issue
1
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Public Library of Science
external identifiers
  • wos:000255378700006
ISSN
1553-7404
DOI
10.1371/journal.pgen.0030236
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English
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yes
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36232657-67af-4144-9f1c-f72855efa1de (old id 1205013)
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2008-09-18 13:08:37
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@article{36232657-67af-4144-9f1c-f72855efa1de,
  abstract     = {European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false-positive or false-negative associations due to population stratification and to identify genetic variants whose contribution to disease risk differs across European ancestries. Here, we investigate empirical patterns of population structure in European Americans, analyzing 4,198 samples from four genome-wide association studies to show that components roughly corresponding to northwest European, southeast European, and Ashkenazi Jewish ancestry are the main sources of European American population structure. Building on this insight, we constructed a panel of 300 validated markers that are highly informative for distinguishing these ancestries. We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data.},
  articleno    = {e236},
  author       = {Price, Alkes L. and Butler, Johannah and Patterson, Nick and Capelli, Cristian and Pascali, Vincenzo L. and Scarnicci, Francesca and Ruiz-Linares, Andres and Groop, Leif and Saetta, Angelica A. and Korkolopoulou, Penelope and Seligsohn, Uri and Waliszewska, Alicja and Schirmer, Christine and Ardlie, Kristin and Ramos, Alexis and Nemesh, James and Arbeitman, Lori and Goldstein, David B. and Reich, David and Hirschhorn, Joel N.},
  issn         = {1553-7404},
  language     = {eng},
  number       = {1},
  publisher    = {Public Library of Science},
  series       = {PLoS Genetics},
  title        = {Discerning the ancestry of European Americans in genetic association studies},
  url          = {http://dx.doi.org/10.1371/journal.pgen.0030236},
  volume       = {4},
  year         = {2008},
}