Measuring European population stratification with microarray genotype data

Marc Bauchet; Brian McEvoy; Laurel N. Pearson; Ellen E. Quillen; Tamara Sarkisian; Kristine Hovhannesyan; Ranjan Deka; Daniel G. Bradley; Mark D. Shriver

doi:10.1086/513477

Measuring European population stratification with microarray genotype data

Marc Bauchet, Brian McEvoy, Laurel N. Pearson, Ellen E. Quillen, Tamara Sarkisian, Kristine Hovhannesyan, Ranjan Deka, Daniel G. Bradley, Mark D. Shriver

Anthropology

Research output: Contribution to journal › Article › peer-review

139 Scopus citations

Abstract

A proper understanding of population genetic stratification - differences in individual ancestry within a population - is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of ∼10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Étude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.

Original language	English (US)
Pages (from-to)	948-956
Number of pages	9
Journal	American Journal of Human Genetics
Volume	80
Issue number	5
DOIs	https://doi.org/10.1086/513477
State	Published - May 2007

All Science Journal Classification (ASJC) codes

Genetics
Genetics(clinical)

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10.1086/513477

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@article{09b8627febee4c9e9e7252acc0a2af4d,

title = "Measuring European population stratification with microarray genotype data",

abstract = "A proper understanding of population genetic stratification - differences in individual ancestry within a population - is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of ∼10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'{\'E}tude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.",

author = "Marc Bauchet and Brian McEvoy and Pearson, {Laurel N.} and Quillen, {Ellen E.} and Tamara Sarkisian and Kristine Hovhannesyan and Ranjan Deka and Bradley, {Daniel G.} and Shriver, {Mark D.}",

note = "Funding Information: We are grateful to the research subjects and to all who helped by collecting or providing human samples—in particular, S. Alonso, G. Argyropoulos, M. Bamshad, C. Batini, S. Beleza, M. Bower, C. Brady, A. de la Chapelle, V. Coia, G. Destro-Bisol, L. Jorde, R. Kaczanowski, R. Kittles, E. Parra, T. Schurr, and S. Tishkoff. We thank Dr. Zaykin for providing the program to calculate the combined P value. We thank our financial supporters: National Institutes of Health National Human Genome Research Institute grant HG002154, Science Foundation of Ireland Walton fellowship 04/W4/B643 (to M.D.S.), Health Research Board-Ireland grant RP/2004/155 (to B.M.), and the Hill and Weiss fellowships (to M.B.). ",

year = "2007",

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language = "English (US)",

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AU - Bauchet, Marc

AU - McEvoy, Brian

AU - Pearson, Laurel N.

AU - Quillen, Ellen E.

AU - Sarkisian, Tamara

AU - Hovhannesyan, Kristine

AU - Deka, Ranjan

AU - Bradley, Daniel G.

AU - Shriver, Mark D.

N1 - Funding Information: We are grateful to the research subjects and to all who helped by collecting or providing human samples—in particular, S. Alonso, G. Argyropoulos, M. Bamshad, C. Batini, S. Beleza, M. Bower, C. Brady, A. de la Chapelle, V. Coia, G. Destro-Bisol, L. Jorde, R. Kaczanowski, R. Kittles, E. Parra, T. Schurr, and S. Tishkoff. We thank Dr. Zaykin for providing the program to calculate the combined P value. We thank our financial supporters: National Institutes of Health National Human Genome Research Institute grant HG002154, Science Foundation of Ireland Walton fellowship 04/W4/B643 (to M.D.S.), Health Research Board-Ireland grant RP/2004/155 (to B.M.), and the Hill and Weiss fellowships (to M.B.).

PY - 2007/5

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N2 - A proper understanding of population genetic stratification - differences in individual ancestry within a population - is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of ∼10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Étude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.

AB - A proper understanding of population genetic stratification - differences in individual ancestry within a population - is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of ∼10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Étude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.

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Measuring European population stratification with microarray genotype data

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