The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia
ABSTRACT: We genotyped 322 new samples from 38 Eurasian populations and combined it with previously published data to characterize the population structure of Turkic-speaking populations in the context of their geographic neighbors across Eurasia 322 samples were analysed with the Illumina Human610-Quad, Human660W-Quad, and HumanOmni1-Quad Genotyping BeadChips and are described herein.
Project description:Here we present genome-wide high-coverage genotyping data on a panel of 85 human samples from Eurasia that are used in addition to public data in studing the genomic context of a 24 kya old DNA sample from Southern Siberia that was sequenced to the avwerage depth of 1X. 85 samples were analysed with the Illumina platforms Human610-Quad v1.0, HumanHap650Yv3 (HumanHap650Yv3_A) and Human660W-Quad v1.0 Genotyping BeadChips and are described herein.
Project description:Sakha – an area connecting South and Northeast Siberia – is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia. We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia. Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia. 40 samples were analysed with the Illumina platform Human660W-Quad v1.0 and are described herein.
Project description:Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci. 24 samples were analysed with the Illumina platform Human660W-Quad v1.0 Genotyping BeadChip and are described herein.
Project description:To carry out population genetics analyses of the Arctic gregion we carried out Illumina Bead-Array-based enotyping on 18 samples from Greenland. 19 samples were analysed with the Illumina platform Human660W-Quad v1.0 Genotyping BeadChip and are described herein.
Project description:Here we present genome-wide high-coverage genotyping data on a panel of 75 human samples from Western Balkan region, Europe, that are used in addition to public data in studing the genetic variation of Southern Europe that was sequenced to the avwerage depth of 1X. 70 samples were analysed with the Illumina platform Human660W-Quad v1.0 Genotyping BeadChip and are described herein.
Project description:The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture. 204 samples were analysed with the Illumina platform Human610-Quad v 1.0 and are described herein.
Project description:Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars - a Slavic-speaking Sunni-Muslim ethno-religious minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territories via several migration waves, mainly from the Golden Horde. Our results show that Belarusian Lipka Tatars share a substantial part of their gene pool with Europeans as indicated by their Y-chromosomal, mitochondrial DNA and autosomal variation. Nevertheless, Belarusian Lipkas still retain a strong genetic signal of their nomadic ancestry, witnessed by the presence of common Y-chromosomal and mitochondrial DNA variants as well as autosomal segments identical by descent between Lipkas and East Eurasians from temperate and northern regions. Hence, we document Lipka Tatars as a unique example of former Medieval migrants into Central Europe, who became sedentary, changed language to Slavic, yet preserved their faith and retained, both uni- and bi-parentally, a clear genetic echo of a complex population interplay throughout the Eurasian Steppe Belt, extending from Central Europe to northern China. 6 samples were analysed with the Illumina platform HumanOmniExpress-24 v1.0 BeadChip and are described herein. Please note that the submitted information does not compromise participant privacy and is in accord with the original consent in addition to all applicable laws, regulations, and institutional policies. The submitter verified that there are no privacy concerns and that our human data can be open access.
Project description:To study the population genetic structure and genome-wide signals of positive selection we carried out Illumina genotyping for 142 individuals of Sout Asian origin 142 samples are analysed on thwo different Illumina platforms. 48 of them with Human610-Quad v 1.0 are described herein. 142 samples are analysed on thwo different Illumina platforms. 94 of them with HumanHap650Yv3_A are described herein.
Project description:The search for novel oncogenes is important because these could be the target of future specific anticancer therapies. In the present work, we report the identification of novel amplified genes in lung cancer. In order to find out novel amplified genes in lung cancer, we aligned the gene expression data of 69 human lung tumors according to the position of transcripts in the human genome and searched for clusters of overexpressed genes. We found a cluster in chromosomes 13q34 and 11q12 with gene overexpression in four of these tumors. Then, we performed FISH analysis in these amplicons, which clearly evidenced the presence of high level copy number in these chromosomal regions. We performed SNP arrays-based in the tumors that carried gene amplification. The results clearly evidenced the presence of a high level copy number amplicon in these specimens. We determined the genomic copy number profile of four squamous cell carcinoma (SCC) tumours using a SNP array, the Illumina Infinium HumanOmni1-Quad BeadChip.
Project description:Here we present genome-wide high-coverage genotyping data on a panel of 85 human samples from Eurasia that are used in addition to public data in studing the genomic context of a 24 kya old DNA sample from Southern Siberia that was sequenced to the avwerage depth of 1X. Overall design: 85 samples were analysed with the Illumina platforms Human610-Quad v1.0, HumanHap650Yv3 (HumanHap650Yv3_A) and Human660W-Quad v1.0 Genotyping BeadChips and are described herein.