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Thread: A Genetic Study on 16 Turks from Different Parts of Turkey

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    Veteran Member Hudayar's Avatar
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    Default A Genetic Study on 16 Turks from Different Parts of Turkey

    Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa
    https://bmcgenomics.biomedcentral.co...71-2164-15-963





    According to the study, Turks cluster with Southern Europeans, however, the weights for the migration events predicted to originate from the East Asian branch into current-day Turkey was 0.217 which mean that modern day Turks carry 21.7% Asian dna in them.








    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.

    Although the 1000 Genomes Project published in 2012 [2] had aimed to provide a comprehensive map of human genetic variation, it was not complete: populations in the Eastern Mediterranean and the Middle East were missing from that study. In this paper, we present data from high depth whole genome sequencing of 16 individuals from modern day Turkey to complement the 1000 Genomes Project in an effort to extend our understanding of normal human genetic variation. We provide the first preliminary genome-wide map of single nucleotide variation, as well as deletion polymorphisms in this population and in western Asia.

    Our analyses show that genetic variation of the contemporary Turkish population is best described within the context of the Southern European/Mediterranean gene pool. However, we predict notable genetic sharing between Turkey’s population and East Asian and African populations. As expected from recent studies, rare and private genetic variation in Turkey has presumably more functional impact than variation shared among populations. We further identified SNPs that were previously associated with diseases that show allele frequency differentiation between Turkey and other Western European populations. Among these, those associated with pigmentation were at lower frequencies in Turkey than in Europe; meanwhile variants associated with total cholesterol levels were at higher levels in the former. Overall, our study improves the framework for population genomics studies in the region, and should incite novel genome-wide association studies in Turkey. Future studies using larger sample sizes will be able to elucidate population structure and history in more detail.




    16 Turks were selected from these parts of Turkey
    Last edited by Hudayar; 09-29-2017 at 05:05 PM.

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    Veteran Member Hudayar's Avatar
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    I think they should've also included Turks from Aydın, Giresun, Sivas, Gaziantep and Thrace (Edirne, Kırklareli, Tekirdağ and Thracian part of Çanakkale). I'm curious about their genetic make-up.


    Also can we actually get the genetic samples from that study, upload them to Gedmatch? I've been looking for Turkish gedmatch results for the last 3 days but only found one with a Gedmatch kitnumber.
    Last edited by Hudayar; 09-29-2017 at 09:21 PM.

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    They have only included samples from 1000 Genomes Project who covers only a very small portion of Europe and the rest of the world. It's a very poor sampling. They even admit that:

    "Although the 1000 Genomes Project published in 2012 [2] had aimed to provide a comprehensive map of human genetic variation, it was not complete: populations in the Eastern Mediterranean and the Middle East were missing from that study"

    Studies like this are pretty useless imo.

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    Quote Originally Posted by Percivalle View Post
    They have only included samples from 1000 Genomes Project who covers only a very small portion of Europe and the rest of the world. It's a very poorly sampling. They even admit that:

    "Although the 1000 Genomes Project published in 2012 [2] had aimed to provide a comprehensive map of human genetic variation, it was not complete: populations in the Eastern Mediterranean and the Middle East were missing from that study"

    Studies like this are pretty useless imo.
    I agree with you about the samples. There are only Southern Europeans, Northern Europeans, Africans and East Asians/Amerindians in the study. Turks will obviously cluster with Southern Europeans (even though i think we're still not close to Southern Europeans genetically in any way). On the other hand, it's not "useless". It's pretty good to see how much Asian shifted are modern-day Turks. Seems it ranges from 5% to 22% (or more).

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    They "cluster" with southern Europeans because they only have African, European and east Asian populations. If you zoom in further, you can see that they're genetically quite far away from Europeans on average.

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    Yeah. I'm aware of that. Read what i wrote above you. We can consider Europeans as pure caucasoids, East Asians as pure mongoloids and Africans as pure Negroids. The chart works better as a racial chart than as an ethnic one imo.

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    Quote Originally Posted by Hudayar View Post
    I agree with you about the samples. There are only Southern Europeans, Northern Europeans, Africans and East Asians/Amerindians in the study. Turks will obviously cluster with Southern Europeans (even though i think we're still not close to Southern Europeans genetically in any way). On the other hand, it's not "useless". It's pretty good to see how much Asian shifted are modern-day Turks. Seems it ranges from 5% to 22% (or more).
    Has not it been calculated yet? I remember an old study that estimated around 14%. But I think there is a big variability in Turkey. Correct me if I'm wrong.

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    Veteran Member Hudayar's Avatar
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    Quote Originally Posted by Percivalle View Post
    Has not it been calculated yet? I remember an old study that estimated around 14%. But I think there is a big variability in Turkey. Correct me if I'm wrong.
    It was not calculated "officially" as far as i know. Also yes you're right. There's a big variability in Turkish asiatic dna. For example people from Northeastern Turkey, as far as i saw, have 0% to 3% mongoloid dna which didn't surprise me actually because in Turkey if a guy from those provinces pisses of someone he'll get called "Rum Dönmesi" which means "Greek convert" or something like that. But Turks from other provinces on average have 14-16% mongoloid dna. Most mongoloid Turks are either Yörüks or people from Giresun (22% mongoloid) as far as i know. Some Turks from isolated villages could score more than that or identical to that i think.
    Last edited by Hudayar; 09-29-2017 at 06:35 PM.

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    Quote Originally Posted by Hudayar View Post
    It was not calculated "officially" as far as i know. Also yes you're right. There's a big variability in Turkish asiatic dna. For example people from Northeastern Turkey, as far as i saw, have 0% to 3% mongoloid dna which didn't surprise me actually because in Turkey if a guy from those provinces pisses of someone he'll get called "Rum Dönmesi" which means "Greek convert" or something like that. But Turks from other provinces on average have 14-16% mongoloid dna. Most mongoloid Turks are either Yörüks or people from Giresun (22% mongoloid) as far as i know. Some Turks from isolated villages could score more than that or identical to that i think.
    The average for Turkey should be 7% as far as I know. Yörüks are not that many.

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    Quote Originally Posted by Fedora View Post
    The average for Turkey should be 7% as far as I know. Yörüks are not that many.
    According to the spreadsheet and genetic results that i saw the average is around 14% 15% and sometimes 12% 13%. it's never below 10%. Only Balkan Turks score 5% 7% as far as i know.

    besides, the study that i posted also proves it. but they should have also included Turks from the provinces that i mentioned in my second post in this thread.
    Last edited by Hudayar; 09-29-2017 at 10:45 PM.

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