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Thread: The genetic structure of Turkey

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    The genetic structure of Turkey

    The genetic structure of the Turkish population reveals high levels of variation and admixture
    M. Ece Kars, A. Nazlı Başak, O. Emre Onat, Kaya Bilguvar, Jungmin Choi, Yuval Itan, Caner Çağlar, Robin Palvadeau, Jean-Laurent Casanova, David N. Cooper, Peter D. Stenson, Alper Yavuz, Hakan Buluş, Murat Günel, Jeffrey M. Friedman, and Tayfun Özçelik

    Significance
    We delineated the fine-scale genetic structure of the Turkish population by using sequencing data of 3,362 unrelated Turkish individuals from different geographical origins and demonstrated the position of Turkey in terms of human migration and genetic drift. The results show that the genetic structure of present-day Anatolia was shaped by historical and modern-day migrations, high levels of admixture, and inbreeding. We observed that modern-day Turkey has close genetic relationships with the neighboring Balkan and Caucasus populations. We generated a Turkish Variome which defines the extent of variation observed in Turkey, listed homozygous loss-of-function variants and clinically relevant variants in the cohort, and generated an imputation panel for future genome-wide association studies.

    Abstract
    The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.

    Supplimentary Data can be downloaded here, does not appear to require a subscription:
    https://www.pnas.org/content/118/36/...b-figures-data

    This spreadsheet contains the sample haplogroups:
    https://www.pnas.org/highwire/filest...6118.sd01.xlsx

    Principal Component Analysis, ADMIXTURE, Haplogroup maps and details are in the Appendix:
    https://www.pnas.org/content/pnas/su...76118.sapp.pdf
    Last edited by pmokeefe; 08-23-2021 at 08:48 PM.
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    The Distribution of Y Chromosome and Mitochondrial DNA Haplotypes.

    The Distribution of Y Chromosome and Mitochondrial DNA Haplotypes. (from the paper)
    Y chromosome and mitochondrial DNA (mtDNA) haplogroup analyses largely confirmed close genetic connections between the TR and EUR populations as well as with the neighboring populations. The most common Y chromosome haplogroups in TR individuals were from J2a (18.4%), R1b (14.9%), and R1a (12.1%) sublineages, consistent with previous findings (SI Appendix, Fig. S12 and Dataset S1) (3). Except for TR-B, in which I2a (20%) was the most prevalent haplogroup followed by R2a (17.1%) and E1b (14.3%), Y chromosome haplogroup distribution was similar with small differences in the TR subregions (SI Appendix, Fig. S13). For the mtDNA, the most common haplogroups were from the H sublineage (27.55%) followed by haplogroup U (19.53%) and haplogroup T (10.99%) in the TR population, as would be expected (SI Appendix, Fig. S14 and Dataset S1) (26). mtDNA haplogroup distribution showed small variance in the TR subregions, except for TR-B in which the frequency of the T haplogroup was very low (SI Appendix, Fig. S15). We also investigated the paternal and maternal gene flow from Central Asia by using the frequency of haplogroups that are restricted to Central Asia (3). Paternal gene flow based on Y chromosome haplogroups C-RPS4Y and O3-M122, which were previously implicated as Central Asian specific, ranged from 8.5 to 15.6%. Maternal gene flow based on mtDNA haplogroups D4c and G2a, which were previously suggested as Central Asian specific, was 8.13% (27) (SI Appendix, Population Structure Analysis).

    pnas.2026076118.jpg
    Fig. S13. Y-haplogroup distribution in the TR subregions. The pie charts demonstrate the Y
    chromosome haplogroups of TR males with known ancestral origin (n = 370). Only main
    haplogroups are shown.

    pnas.2026076118.jpg
    Fig. S15. mtDNA-haplogroup distribution in the TR subregions. The pie charts demonstrate
    the mt-DNA haplogroups of TR individuals with known ancestral origin (n = 647). Only main
    haplogroups are shown.
    Last edited by pmokeefe; 08-23-2021 at 09:27 PM.
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    Population Structure of Turkey

    Population Structure of Turkey. (from the paper)

    Additionally, we calculated the Central Asian contribution to the modern-day TR population as 9.59% based on ADMIXTURE results. This contribution varied for the TR subregions: TR-B, 7.69%; TR-W, 12%; TR-C, 10.1%; TR-N, 10.6%; TR-S, 11.2%; and TR-E, 6.48%.

    The geographical origins of ancestors (birthplaces of maternal and paternal grandparents) of 1,460 TR samples were documented and grouped into six different subregions, namely Balkan (TR-B: 90), West (TR-W: 157), Central (TR-C: 441), North (TR-N: 372), South (TR-S: 116), and East (TR-E: 284)
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    The paper is finally out

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    I guess the notion that the Seljuks brought an inordinate amount of Central Asian admixture can be officially debunked. I'm wondering how modern Turks feel about this. They are certainly progeny of those great Anatolian civilizations; Hittites, Lydians, Phrygians, etc.

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    Interesting/puzzling that in the paper there is only 12 x T1 ydna ( 10 x T1a1 branch and 2 x T1a2 branch )

    An armenian paper many years ago had 22% of T1 around lake Van area

    so....did this paper test Kurds and Armenians?

    History of Van area is with the Kingdom of Van which is linked to ancient Urartu kingdom and their Alarodian languages

    https://en.wikipedia.org/wiki/Alarodian_languages

    There are a few ancient T1 samples around the caspian sea


    Are Armenians and Kurds distant cousins? .....................cousins of Kurds are the Zaza, Yezidi and Azeri people


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+, Y349970+, Y79536+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna

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    Data Availability

    Data Availability
    Turkish Variome and Turkish reference panels for imputation are available for download from Figshare at https://figshare.com/articles/datase...xture/15147642. Individual level WES and WGS data are available at the Sequence Read Archive repository BioProject (accession ID: PRJNA670444, PRJNA674530, and PRJNA624188) and dbGAP under accession phs000744.v4.p2.
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    Quote Originally Posted by TonyC View Post
    I guess the notion that the Seljuks brought an inordinate amount of Central Asian admixture can be officially debunked. I'm wondering how modern Turks feel about this. They are certainly progeny of those great Anatolian civilizations; Hittites, Lydians, Phrygians, etc.
    maybe....the Seljuks only arrived a 1000 years ago

    we should include assyrians and maybe even Medes


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    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna

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    Quote Originally Posted by vettor View Post
    Interesting/puzzling that in the paper there is only 12 x T1 ydna ( 10 x T1a1 branch and 2 x T1a2 branch )

    An armenian paper many years ago had 22% of T1 around lake Van area

    so....did this paper test Kurds and Armenians?

    History of Van area is with the Kingdom of Van which is linked to ancient Urartu kingdom and their Alarodian languages

    https://en.wikipedia.org/wiki/Alarodian_languages

    There are a few ancient T1 samples around the caspian sea


    Are Armenians and Kurds distant cousins? .....................cousins of Kurds are the Zaza, Yezidi and Azeri people
    Looking at this map T1a is significantly higher in TR-E (Eastern Turkey) then in the other regions.

    pnas.2026076118.jpg
    Last edited by pmokeefe; 08-23-2021 at 11:45 PM.
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    Quote Originally Posted by vettor View Post
    Interesting/puzzling that in the paper there is only 12 x T1 ydna ( 10 x T1a1 branch and 2 x T1a2 branch )

    An armenian paper many years ago had 22% of T1 around lake Van area

    so....did this paper test Kurds and Armenians?

    History of Van area is with the Kingdom of Van which is linked to ancient Urartu kingdom and their Alarodian languages

    https://en.wikipedia.org/wiki/Alarodian_languages

    There are a few ancient T1 samples around the caspian sea


    Are Armenians and Kurds distant cousins? .....................cousins of Kurds are the Zaza, Yezidi and Azeri people
    People's autosomal analyses earlier this year showed that there were definitely Kurds and Assyrians, and maybe Armenians, in the sample set.
    The clock indicates the moment—but what does eternity indicate?

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