Genetic structure of europeans: A view from the north-east

Mari Nelis, Tõni Esko, Reedik Mägi, Fritz Zimprich, Draga Toncheva, Sena Karachanak, Tereza Piskáčková, Ivan Balaščák, Leena Peltonen, Eveliina Jakkula, Karola Rehnström, Mark Lathrop, Simon Heath, Pilar Galan, Stefan Schreiber, Thomas Meitinger, Arne Pfeufer, H. Erich Wichmann, Béla Melegh, Noémi PolgárDaniela Toniolo, Paolo Gasparini, Pio D'Adamo, Janis Klovins, Liene Nikitina-Zake, Vaidutis Kučinskas, Jurate Kasnauskiene, Jan Lubinski, Tadeusz Debniak, Svetlana Limborska, Andrey Khrunin, Xavier Estivill, Raquel Rabionet, Sara Marsal, Antonio Juliá, Stylianos E. Antonarakis, Samuel Deutsch, Christelle Borel, Homa Attar, Maryline Gagnebin, Milan Macek, Michael Krawczak, Maido Remm, Andres Metspalu

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Abstract

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (F5t) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS). Copyright:

Original languageEnglish
Article numbere5472
JournalPloS one
Volume4
Issue number5
DOIs
Publication statusPublished - 8 May 2009

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ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Nelis, M., Esko, T., Mägi, R., Zimprich, F., Toncheva, D., Karachanak, S., Piskáčková, T., Balaščák, I., Peltonen, L., Jakkula, E., Rehnström, K., Lathrop, M., Heath, S., Galan, P., Schreiber, S., Meitinger, T., Pfeufer, A., Wichmann, H. E., Melegh, B., ... Metspalu, A. (2009). Genetic structure of europeans: A view from the north-east. PloS one, 4(5), [e5472]. https://doi.org/10.1371/journal.pone.0005472