1. Genetic structure of Europeans: a view from the North-East
- Author
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Thomas Meitinger, T. Piskackova, Leena Peltonen, Draga Toncheva, Christelle Borel, Sena Karachanak, Liene Nikitina-Zake, Xavier Estivill, Béla Melegh, Daniela Toniolo, Janis Klovins, Mari Nelis, Andrey Khrunin, H-Erich Wichmann, Raquel Rabionet, Michael Krawczak, Ivan Balascak, Stefan Schreiber, Tõnu Esko, Jūratė Kasnauskienė, Alexander Zimprich, Paolo Gasparini, Pilar Galan, Fritz Zimprich, Karola Rehnström, Simon Heath, Pio D'Adamo, Antonio Julià, Sara Marsal, Arne Pfeufer, Stylianos E. Antonarakis, Eveliina Jakkula, Svetlana A. Limborska, Noémi Polgár, Reedik Mägi, Samuel Deutsch, Tadeusz Dębniak, Homa Attar, Jan Lubinski, Vaidutis Kučinskas, Maryline Gagnebin, Mark Lathrop, Milan Macek, Andres Metspalu, Maido Remm, Nelis, M, Esko, T, Mägi, R, Zimprich, F, Zimprich, A, Toncheva, D, Karachanak, S, Piskácková, T, Balascák, I, Peltonen, L, Jakkula, E, Rehnström, K, Lathrop, M, Heath, S, Galan, P, Schreiber, S, Meitinger, T, Pfeufer, A, Wichmann, He, Melegh, B, Polgár, N, Toniolo, D, Gasparini, Paolo, D'Adamo, ADAMO PIO, Klovins, J, NIKITINA ZAKE, L, Kucinskas, V, Kasnauskiene, J, Lubinski, J, Debniak, T, Limborska, S, Khrunin, A, Estivill, X, Rabionet, R, Marsal, S, Julià, A, Antonarakis, Se, Deutsch, S, Borel, C, Attar, H, Gagnebin, M, Macek, M, Krawczak, M, Remm, M, and Metspalu, A.
- Subjects
Population genetics ,Genome-wide association study ,genetic [Human] ,Linkage Disequilibrium ,Fixation index ,0302 clinical medicine ,Gene Frequency ,Principal Component Analysi ,genetics [Single Nucleotide] ,Genetic Marker ,genetic [Linkage Disequilibrium] ,Linkage Disequilibrium: genetics ,ddc:576.5 ,ethnology [Europe] ,Genetics ,0303 health sciences ,education.field_of_study ,Principal Component Analysis ,Multidisciplinary ,Genome ,European Continental Ancestry Group/ genetics ,Single Nucleotide ,Genetics and Genomics/Bioinformatics ,genetic [European Continental Ancestry Group] ,Europe ,Geography ,Genetic structure ,Medicine ,Polymorphism, Single Nucleotide/ genetics ,Research Article ,Human ,Europe: ethnology ,Genetic Markers ,Science ,Population ,European Continental Ancestry Group ,Polymorphism, Single Nucleotide ,White People ,Europe/ethnology ,European Continental Ancestry Group: genetics ,03 medical and health sciences ,Genetics and Genomics/Population Genetics ,Humans ,Linkage Disequilibrium/genetics ,Polymorphism ,education ,Allele frequency ,030304 developmental biology ,Human: genetics ,Single Nucleotide: genetics ,Genetic diversity ,Genome, Human ,Genetics and Genomics/Genome Projects ,Genetic marker ,Evolutionary biology ,Genome, Human/genetics ,030217 neurology & neurosurgery - 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 (lambda) (ranging from 1.00 to 4.21), fixation index (F(st)) (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).
- Published
- 2009