Native American population data based on the Globalfiler ® autosomal STR loci

Ng, Jillian; Oldt, Robert F.; McCulloh, Kelly L.; Weise, Jessica A.; Viray, Joy; Budowle, Bruce; Smith, David Glenn; Kanthaswamy, Sreetharan

doi:10.1016/j.fsigen.2016.06.014

Cited by 14 publications

(10 citation statements)

References 8 publications

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“…The values for matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), power of exclusion (PE) duos, typical paternity index (TPI), gene diversity (GD), and expected heterozygosity (He) were calculated by using the PowerStats software (Ver 1.2, Promega, Madison, WI, USA) [14]. Nei's standard genetic distance between current and previously published reference populations (Law et al, 2002;Berti et al, 2005;Tie et al, 2006;Barni et al, 2007;Deng et al, 2007;Maruyama et al, 2008;Demeter et al, 2010;Stepanov et al, 2010;Zhu et al, 2010;Deng et al, 2011;Kee et al, 2011;Xing et al, 2011;Yoo et al, 2011;Chen et al, 2012;Di Cristofaro et al, 2012;Westen et al, 2012;Gaviria et al, 2013;Hedjazi et al, 2013;Nasibov et al, 2013Nasibov et al, , 2013Park et al, 2013;Bentayebi et al, 2014;Fujii et al, 2014;Almeida et al, 2015;Gurkan et al, 2015;Parolin et al, 2015;Shafique et al, 2015;Shrivastava et al, 2015;Zhang, 2015bZhang, , 2015aZhang et al, 2015;Aguilar-Velázquez et al, 2016;Hossain et al, 2016;Nakamura et al, 2016;Ng et al, 2016;Park et al, 2016;Ramos-González et al, 2016;Ristow et ...…”

Section: Discussionmentioning

confidence: 99%

RETRACTED: The Heart of Silk Road “Xinjiang,” Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

et al. 2021

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The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy–Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.

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Section: Discussionmentioning

confidence: 99%

RETRACTED: The Heart of Silk Road “Xinjiang,” Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

et al. 2021

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“…To comprehensively dissect the genetic background of Shanxi northern-Han Chinese, we first integrated our raw genotyping data (23 STRs) with previously published genotype data from 11 Chinese populations from five Chinese ethnic groups (Han, Hui, Tibetan, Yi, and Uyghur) (He et al, 2018b; Wang et al, 2018a; Chen et al, 2019; Liu et al, 2019). To further explore the genetic relationship of Shanxi Han in the context of the genetic variations from the worldwide or nationwide populations, we subsequently combined our allele frequency of 20 STRs with publicly obtained data from 52 worldwide populations (Westen et al, 2012; Gaviria et al, 2013; Park et al, 2013; Fujii et al, 2014; Almeida et al, 2015; Parolin et al, 2015; Aguilar-Velazquez et al, 2016; Hossain et al, 2016; Ng et al, 2016; Park et al, 2016; Ramos-Gonzalez et al, 2016; Ristow et al, 2016; Vullo et al, 2016; Wang, 2016; Zhang et al, 2016a; Zhang et al, 2016b; Choi et al, 2017; Guerreiro et al, 2017; Jin et al, 2017; Liu et al, 2017; Moyses et al, 2017; Ossowski et al, 2017; Singh and Nandineni, 2017; Taylor et al, 2017; Wu et al, 2017; Yang et al, 2017a; He et al, 2018b; He et al, 2018e; Wang et al, 2018a; Liu et al, 2019) and allele frequency of 19 STRs with previously investigated the allele frequency distribution from 60 Chinese populations (Zhang et al, 2011; Zhang, 2012; Liu et al, 2013; Shen, 2013; Zhang, 2013; Wang, 2014; Wang et al, 2014; Xie, 2014; Hu et al, 2015; Li, 2015; Ruan, 2015; Shen et al, 2015; Wang, 2015; Yin, 2015; Zhang and Chen, 2015; Zhao et al, 2015a; Huang, 2016; Meng, 2016; Wang, 2016; Xiang, 2016; Xiao et al, 2016; Zhao, 2016; Chen et al, 2017; Fu et al, 2017; He et al, 2017a; He et al, 2017c; Jin et al, 2017; Liu, 2017; Lu et al, 2017;…”

Section: Methodsmentioning

confidence: 99%

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

Chen

Luo

et al. 2019

Front. Genet.

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Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.

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“…We performed locus-by-locus pairwise comparisons (F st ) and calculated Nei’s standard genetic distances (R st ) between our three studied populations and 47 previously published worldwide populations (Asian 9,15–29 , North American 30–32 , European 33–36 , Oceanian 37 , South American 38–41 and South African 42 populations) based on allele frequencies of 20 expanded CODIS loci to infer interpopulation similarity and differentiation (Supplementary Tables S10–S13 and Fig. S1).…”

Section: Resultsmentioning

confidence: 99%

Genetic polymorphism and phylogenetic differentiation of the Huaxia Platinum System in three Chinese minority ethnicities

Liu

Wang

et al. 2019

Sci Rep

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Short tandem repeats (STRs) with features of high polymorphism and abundant evolution information play a significant role in genetic applications such as human forensics, anthropology and population genetics. The Huaxia Platinum System was specifically exploited to allow coamplification of all markers in the expanded Combined DNA Index System and the Chinese National Database. Herein, in continuation of our previous studies, 493 unrelated individuals were firstly genotyped to investigate the efficacy of this novel system in three minority ethnicities of China (Hui, Tibetan and Uygur). Additionally, genetic relationships among our three investigated populations and other previously published populations were analyzed using pairwise genetic distances, multidimensional scaling (MDS), principal component analysis (PCA), cladogram and STRUCTURE. The combined match probabilities (CMP) for the Hui, Tibetan and Uygur groups were 1.6894 × 10 −27 , 6.1666 × 10 −27 and 5.0655 × 10 −27 , respectively, and the combined powers of exclusion (CPE) were 0.999999999646627, 0.999999999304935 and 0.999999999433994. Population comparison analysis manifested that the Hui and Tibetan populations had genetic affinities with the Han, Yi and Korean populations, while the Uygur group had a close relationship with the Kazakh population. The aforementioned results suggested that the Huaxia Platinum System is a polymorphic and effective tool that is appropriate for personal identification and population genetics.

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Native American population data based on the Globalfiler ® autosomal STR loci

Cited by 14 publications

References 8 publications

RETRACTED: The Heart of Silk Road “Xinjiang,” Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

RETRACTED: The Heart of Silk Road “Xinjiang,” Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

Genetic polymorphism and phylogenetic differentiation of the Huaxia Platinum System in three Chinese minority ethnicities

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