Mitochondrial DNA variation in Tajiks living in Tajikistan

Ovchinnikov, Igor V.; Malek, Mathew J.; Drees, Kenneth; Kholina, Olga I.

doi:10.1016/j.legalmed.2014.07.009

Cited by 5 publications

(2 citation statements)

References 27 publications

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“…Uyghur display typical admixtures of European and East Asian ancestries by genome-wide analysis, with near-equal parental components (50:50 EUR/EAS) [27]. This is consistent with our CUX result obtained with 27 AIMs Mitochondrial DNA variation analysis of Tajiks living in Tajikistan reveals similar genetic western and eastern admixture [40]. Of course, determining the exact genetic components of these admixed populations requires a more comprehensive genome-wide admixture study.…”

Section: Discussionsupporting

confidence: 88%

A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

Wei

Zhao

et al. 2015

Int J Legal Med

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A single-tube multiplex assay of a small set of ancestry-informative markers (AIMs) for effectively estimating individual ancestry and admixture is an ideal forensic tool to trace the population origin of an unknown DNA sample. We present a newly developed 27-plex single nucleotide polymorphism (SNP) panel with highly robust and balanced differential power to perfectly assign individuals to African, European, and East Asian ancestries. Evaluating 968 previously described intercontinental AIMs from three HapMap population genotyping datasets (Yoruban in Ibadan, Nigeria (YRI); Utah residents with Northern and Western European ancestry from the Centre de'Etude du Polymorphism Humain (CEPH) collection (CEU); and Han Chinese in Beijing, China (CHB)), the best set of markers was selected on the basis of Hardy-Weinberg equilibrium (p > 0.00001), population-specific allele frequency (two of three δ values >0.5), according to linkage disequilibrium (r (2) < 0.2), and capable of being multiplexed in one tube and detected by capillary electrophoresis. The 27-SNP panel was first validated by assigning the ancestry of the 11 populations in the HapMap project. Then, we tested the 27-plex SNP assay with 1164 individuals from 17 additional populations. The results demonstrated that the SNP panel was successful for ancestry inference of individuals with African, European, and East Asian ancestry. Furthermore, the system performed well when inferring the admixture of Eurasians (EUR/EAS) after analyzing admixed populations from Xinjiang (Central Asian) as follows: Tajik (68:27), Uyghur (49:46), Kirgiz (40:57), and Kazak (36:60). For individual analyses, we interpreted each sample with a three-ancestry component percentage and a population match probability sequence. This multiplex assay is a convenient and cost-effective tool to assist in criminal investigations, as well as to correct for the effects of population stratification for case-control studies.

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Section: Discussionsupporting

confidence: 88%

A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

Wei

Zhao

et al. 2015

Int J Legal Med

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“…Several efforts have been done to retrieving the genetic information from ancient mtDNA sequences [12,13]. However, due to various kinds of difficulty in sample collection, only limited samples of highland Tajiks were referred recently [14]. Meanwhile, most studies relied upon partial mtDNA sequences (i.e., Dloop and certain coding regions).…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial genomes uncover the maternal history of the Pamir populations

Peng

Song

et al. 2017

Eur J Hum Genet

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The Pamirs, among the world's highest mountains in Central Asia, are one of homelands with the most extreme high altitude for several ethnic groups. The settlement history of modern humans on the Pamirs remains still opaque. Herein, we have sequenced the mitochondrial DNA (mtDNA) genomes of 382 individuals belonging to eight populations from the Pamirs and the surrounding lowlands in Central Asia. We construct the Central Asian (including both highlanders and lowlanders) mtDNA haplogroup tree at the highest resolution. All the matrilineal components are assigned into the defined mtDNA haplogroups in East and West Eurasians. No basal lineages that directly emanate from the Eurasian founder macrohaplogroups M, N, and R are found. Our data support the origin of Central Asian being the result of East-West Eurasian admixture. The coalescence ages for more than 93% mtDNA lineages in Central Asians are dated after the last glacial maximum (LGM). The post-LGM and/or later dispersals/admixtures play dominant roles in shaping the maternal gene pool of Central Asians. More importantly, our analyses reveal the mtDNA heterogeneity in the Pamir highlanders, not only between the Turkic Kyrgyz and the Indo-European Tajik groups, but also among three highland Tajiks. No evidence supports positive selection or relaxation of selective constraints in the mtDNAs of highlanders as compared to that of lowlanders. Our results suggest a complex history for the peopling of Pamirs by multiple waves of migrations from various genetic resources during different time scales.

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RETRACTED ARTICLE: Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs

et al. 2018

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Inferring an unknown DNA's ancestry using a set of ancestry-informative single nucleotide polymorphisms (SNPs) in forensic science is useful to provide investigative leads. This is especially true when there is no DNA database match or specified suspect. Thus, a set of SNPs with highly robust and balanced differential power is strongly demanded in forensic science. In addition, it is also necessary to build a genotyping database for estimating the ancestry of an individual or an unknown DNA. For the differentiation of Africans, Europeans, East Asians, Native Americans, and Oceanians, the Global Nano set that includes just 31 SNPs was developed by de la Puente et al. Its ability for differentiation and balance was evaluated using the genotype data of the 1000 Genomes Phase III project and the Stanford University HGDP-CEPH. Just 402 samples were genotyped and analyzed as a reference set based on statistical methods. To validate the differentiating capacity using more samples, we developed a single-tube 28-plex SNP assay in which the SNPs were chosen from the 31 allelic loci of the Global AIMs Nano set. Three tri-allelic SNPs used to differentiate mixed-source DNA contribute little to population differentiation and were excluded here. Then, 998 individuals from 21 populations were typed, and these genotypes were combined with the genotype data obtained from 1000 Genomes Phase III and the Stanford University HGDP-CEPH (3090 total samples,43 populations) to estimate the power of this multiplex assay and build a database for the further inference of an individual or an unknown DNA sample in forensic practice.

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Mitochondrial DNA variation in Tajiks living in Tajikistan

Cited by 5 publications

References 27 publications

A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

Mitochondrial genomes uncover the maternal history of the Pamir populations

RETRACTED ARTICLE: Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs

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