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      Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

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      Author
      Alkan C.
      Kavak, P.
      Somel, M.
      Gokcumen, O.
      Ugurlu, S.
      Saygi, C.
      Dal, E.
      Bugra, K.
      Güngör, T.
      Sahinalp, S. C.
      Özören, N.
      Bekpen, C.
      Date
      2014-11-07
      Source Title
      BMC Genomics
      Print ISSN
      1471-2164
      Publisher
      BioMed Central Ltd.
      Volume
      15
      Issue
      963
      Pages
      1 - 12
      Language
      English
      Type
      Article
      Item Usage Stats
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      Abstract
      Background: Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32 × −48×). Results: We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency. Conclusion: This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey.
      Keywords
      Genome project
      European population
      Familial mediterranean fever
      Turkish population
      Whole genome shotgu
      Diversity
      Variants
      DNA
      Discovery
      Haplotype
      Permalink
      http://hdl.handle.net/11693/12705
      Published Version (Please cite this version)
      http://dx.doi.org/10.1186/1471-2164-15-963
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      • Department of Computer Engineering 1368
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