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khanabadoshi
09-11-2021, 11:17 AM
https://www.pnas.org/content/118/36/e2026076118


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, Tayfun Özçelik
PNAS September 7, 2021 118 (36) e2026076118; https://doi.org/10.1073/pnas.2026076118

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.


Have the samples from this study been extracted/uploaded? There are a lot of Turkish samples here....



Dataset posted on 26.08.2021, 21:37 :: https://figshare.com/articles/dataset/The_genetic_structure_of_the_Turkish_population_re veals_high_levels_of_variation_and_admixture/15147642

Turkish Variome contains allele frequencies of 46,739,479 variants of 3,362 unrelated Turkish individuals.

Turkish reference panel for imputation contains phased haplotypes of 773 whole-genome sequenced unrelated Turkish individuals.

Plink files of 1,460 origin-known Turkish individuals. These files contain 423,261 variants that were used for population structure analyses.



Kars, Meltem Ece; Basak, Ayse Nazli; Onat, Onur Emre; Bilguvar, Kaya; Choi, Jungmin; Itan, Yuval; et al. (2021): The genetic structure of the Turkish population reveals high levels of variation and admixture. figshare. Dataset. https://doi.org/10.6084/m9.figshare.15147642.v4

pmokeefe
09-11-2021, 12:58 PM
There's another discussion thread for that paper here: https://anthrogenica.com/showthread.php?24591-The-genetic-structure-of-Turkey