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

Date
2014-11-07
Authors
Alkan C.
Kavak, P.
Somel, M.
Gokcumen, O.
Ugurlu, S.
Saygi, C.
Dal, E.
Bugra, K.
Güngör, T.
Sahinalp, S. C.
Advisor
Supervisor
Co-Advisor
Co-Supervisor
Instructor
Source Title
BMC Genomics
Print ISSN
1471-2164
Electronic ISSN
Publisher
BioMed Central Ltd.
Volume
15
Issue
963
Pages
1 - 12
Language
English
Type
Article
Journal Title
Journal ISSN
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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.

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Keywords
Genome project, European population, Familial mediterranean fever, Turkish population, Whole genome shotgu, Diversity, Variants, DNA, Discovery, Haplotype
Citation
Published Version (Please cite this version)