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

Date

2014-03-01

Author

Gokcumen, Omer
Alkan, Can
Kavak, Pinar
Somel, Mehmet
Ugurlu, Serkan
Dal, Elif
Bugra-Bilge, Kuyas
Gungor, Tunga
Sahinalp, Cenk
Ozeren, Nesrin
Bekpen, Cemalettin

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

235
views

0
downloads

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

Subject Keywords

Anthropology, Evolutionary biology

URI

https://hdl.handle.net/11511/55947

Collections

Department of Biology, Conference / Seminar

Suggestions

OpenMETU
Core

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa Alkan, Can; Kavak, Pinar; Somel, Mehmet; Gokcumen, Omer; Ugurlu, Serkan; Saygi, Ceren; Dal, Elif; Bugra, Kuyas; GÜNGÖR, TUNGA; Sahinalp, S. Cenk; ÖZÖREN, NESRİN; BEKPEN, CEMALETTİN (2014-11-07) 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 x -48x).
DNA diversity and population admixture in Anatolia Di Benedetto, G; Erguven, A; Stenico, M; Castri, L; Bertorelle, G; Togan, İnci Zehra; Barbujani, G (Wiley, 2001-06-01) The Turkic language was introduced in Anatolia at the start of this millennium, by nomadic Turk-men groups from Central Asia. Whether that cultural transition also had significant population-genetics consequences is not fully understood. Three nuclear microsatellite loci, the hypervariable region I of the mitochondrial genome, six microsatellite loci of the Y chromosome, and one Alu insertion (YAP) were amplified and typed in 118 individuals from four populations of Anatolia. For each locus, the number of c...
Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data Debortoli, Guilherme; Abbatangelo, Cristina; Ceballos, Francisco; Fortes-Lima, Cesar; Norton, Heather L.; Ozarkar, Shantanu; Parra, Esteban J.; Jonnalagadda, Manjari (Springer Science and Business Media LLC, 2020-6-22) The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective popul...
Comparative analyses for the Central Asian contribution to Anatolian gene pool with reference to Balkans Berkman, Ceren Caner; Togan, İnci Zehra; Department of Biology (2006) Around 1000 ya, Turkic language started to be introduced to Turkey and Azerbaijan (Region of language replacement, RLR) in parallel with the migrations of Turkic speaking nomadic groups from Central Asia. The Central Asian contribution to the RLR was analyzed with four admixture methods considering different evolutionary forces. Furthermore, the association between the Central Asian contribution and the language replacement episode was estimated by comparatively analyzing the Central Asian contribution to R...
Critical evaluation of “adjacent areas” concept from urban growth perspective in Turkish urban planning: the case of Ankara Yıldırım, Sibel; Keskinok, Hüseyin Çağatay; Department of City and Regional Planning (2008) The effects of expansion of cities on the fringe area are still the common problems of several countries as well as Turkey. The main problem stemming from rapid urban growth was described as urban sprawl that has been used as waste of land, time, and natural resources. Although sprawl becomes usually unplanned, uncontrolled, and uncoordinated, it can be claimed that some local and national government policies triggers the urban sprawl by creating planned areas more than required. The growth management polic...

Citation Formats

O. Gokcumen et al., “Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa,” 2014, vol. 153, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/55947.