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Inferring Geographic Coordinates of Origin for Europeans Using Small Panels of Ancestry Informative Markers

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  • Petros Drineas
  • Jamey Lewis
  • Peristera Paschou

Abstract

Recent large-scale studies of European populations have demonstrated the existence of population genetic structure within Europe and the potential to accurately infer individual ancestry when information from hundreds of thousands of genetic markers is used. In fact, when genomewide genetic variation of European populations is projected down to a two-dimensional Principal Components Analysis plot, a surprising correlation with actual geographic coordinates of self-reported ancestry has been reported. This substructure can hamper the search of susceptibility genes for common complex disorders leading to spurious correlations. The identification of genetic markers that can correct for population stratification becomes therefore of paramount importance. Analyzing 1,200 individuals from 11 populations genotyped for more than 500,000 SNPs (Population Reference Sample), we present a systematic exploration of the extent to which geographic coordinates of origin within Europe can be predicted, with small panels of SNPs. Markers are selected to correlate with the top principal components of the dataset, as we have previously demonstrated. Performing thorough cross-validation experiments we show that it is indeed possible to predict individual ancestry within Europe down to a few hundred kilometers from actual individual origin, using information from carefully selected panels of 500 or 1,000 SNPs. Furthermore, we show that these panels can be used to correctly assign the HapMap Phase 3 European populations to their geographic origin. The SNPs that we propose can prove extremely useful in a variety of different settings, such as stratification correction or genetic ancestry testing, and the study of the history of European populations.

Suggested Citation

  • Petros Drineas & Jamey Lewis & Peristera Paschou, 2010. "Inferring Geographic Coordinates of Origin for Europeans Using Small Panels of Ancestry Informative Markers," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-6, August.
  • Handle: RePEc:plo:pone00:0011892
    DOI: 10.1371/journal.pone.0011892
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    References listed on IDEAS

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    1. Peristera Paschou & Petros Drineas & Jamey Lewis & Caroline M Nievergelt & Deborah A Nickerson & Joshua D Smith & Paul M Ridker & Daniel I Chasman & Ronald M Krauss & Elad Ziv, 2008. "Tracing Sub-Structure in the European American Population with PCA-Informative Markers," PLOS Genetics, Public Library of Science, vol. 4(7), pages 1-13, July.
    2. Peristera Paschou & Elad Ziv & Esteban G Burchard & Shweta Choudhry & William Rodriguez-Cintron & Michael W Mahoney & Petros Drineas, 2007. "PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations," PLOS Genetics, Public Library of Science, vol. 3(9), pages 1-15, September.
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    Cited by:

    1. Paola Raska & Edwin Iversen & Ann Chen & Zhihua Chen & Brooke L Fridley & Jennifer Permuth-Wey & Ya-Yu Tsai & Robert A Vierkant & Ellen L Goode & Harvey Risch & Joellen M Schildkraut & Thomas A Seller, 2012. "European American Stratification in Ovarian Cancer Case Control Data: The Utility of Genome-Wide Data for Inferring Ancestry," PLOS ONE, Public Library of Science, vol. 7(5), pages 1-9, May.
    2. Gustavo de los Campos & Yann C Klimentidis & Ana I Vazquez & David B Allison, 2012. "Prediction of Expected Years of Life Using Whole-Genome Markers," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-7, July.

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