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08-23-2021, 08:54 PM
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.
https://www.pnas.org/content/118/36/e2026076118
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.
https://www.pnas.org/content/118/36/e2026076118