PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile

Pereira, Luı́sa; Alshamali, Farida; Andreassen, Rune; Ballard, Ruth E.; Chantratita, Wasun; Cho, Nam Soo; Coudray, Clotilde; Dugoujon, Jean Michel; Espinoza, Marta; González-Andrade, Fabricio; Hadi, Sibte; Immel, Uta Dorothee; Marian, Cătălin; González‐Martín, Antonio; Mertens, Gerhard; Parson, Walther; Perone, Carlos; Prieto, Lourdes; Takeshita, Hitoshi; Rangel-Villalobos, Héctor; Zeng, Zhaoshu; Zhivotovsky, Lev A.; Camacho, Rui; Fonseca, Nuno A.

doi:10.1007/s00414-010-0472-2

Cited by 44 publications

(24 citation statements)

References 39 publications

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“…Tests for Hardy–Weinberg equilibrium were performed in Arlequin v3.5.1.319. Since the statistical analyses in this study were on the basis of Bayesian-clustering algorithm, raw genotypic data of 13 STRs (excluding D6S1043 and D12S391) from 59 populations all around the world were extracted to determine population affinity1420212223242526272829303132333435363738394041424344454647484950. Analysis of molecular variance (AMOVA), average number of pairwise differences, pairwise Fst, Slatkins linearized Fst, and coancestry coefficients were all calculated in Arlequin v3.5.1.319 using genotype data.…”

Section: Methodsmentioning

confidence: 99%

Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci

Yao

Wang

et al. 2017

Sci Rep

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The origin and diversification of Sino-Tibetan speaking populations have been long-standing hot debates. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal short tandem repeats (STRs) from 803 unrelated Tibetan individuals from Gansu Province (635 from Gannan and 168 from Tianzhu) in northwest China. We combined these data with published dataset to infer a detailed population affinities and genetic substructure of Sino-Tibetan populations. Our results revealed Tibetan populations in Gannan and Tianzhu are genetically very similar with Tibetans from other regions. The Tibetans in Tianzhu have received more genetic influence from surrounding lowland populations. The genetic structure of Sino-Tibetan populations was strongly correlated with linguistic affiliations. Although the among-population variances are relatively small, the genetic components for Tibetan, Lolo-Burmese, and Han Chinese were quite distinctive, especially for the Deng, Nu, and Derung of Lolo-Burmese. Han Chinese but not Tibetans are suggested to share substantial genetic component with southern natives, such as Tai-Kadai and Hmong-Mien speaking populations, and with other lowland East Asian populations, which implies there might be extensive gene flow between those lowland groups and Han Chinese after Han Chinese were separated from Tibetans. The dataset generated in present study is also valuable for forensic identification and paternity tests in China.

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Section: Methodsmentioning

confidence: 99%

Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci

Yao

Wang

et al. 2017

Sci Rep

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“…Tests for Hardy–Weinberg equilibrium (HWE) were performed in Arlequin v3.5.1.312 using a likelihood ratio test and an exact test to prevent miscalling STR genotypes or biased sampling. Since the statistical analyses in this study were on the basis of Bayesian-clustering algorithm, raw genotypic data of 13 STRs (excluding D6S1043 and D12S391) from 45 populations (13793 individuals) all around the world were extracted to determine population affinity131415161718192021222324252627282930313233343536373839. Average number of pairwise differences, pairwise Fst, Slatkins linearized Fst, and coancestry coefficients were all calculated in Arlequin v3.5.1.3 using genotype data12.…”

Section: Methodsmentioning

confidence: 99%

Genetic evidence for an East Asian origin of Chinese Muslim populations Dongxiang and Hui

Yao

Wang

Tao

et al. 2016

Sci Rep

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There is a long-going debate on the genetic origin of Chinese Muslim populations, such as Uygur, Dongxiang, and Hui. However, genetic information for those Muslim populations except Uygur is extremely limited. In this study, we investigated the genetic structure and ancestry of Chinese Muslims by analyzing 15 autosomal short tandem repeats in 652 individuals from Dongxiang, Hui, and Han Chinese populations in Gansu province. Both genetic distance and Bayesian-clustering methods showed significant genetic homogeneity between the two Muslim populations and East Asian populations, suggesting a common genetic ancestry. Our analysis found no evidence of substantial gene flow from Middle East or Europe into Dongxiang and Hui people during their Islamization. The dataset generated in present study are also valuable for forensic identification and paternity tests in China.

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“…We would like to acknowledge Schlebusch et al [1] for kindly sharing data and also the NRF innovation bursary for funding the writing of this manuscript.…”

Section: Acknowledgementsmentioning

confidence: 98%

“…The genetic differentiation between populations originates from the isolation of groups or selective processes acting upon coding regions. This genetic differentiation makes it possible to assign an individual to a group as implemented in Popaffiliator [1] and STRBASE 2.0 (http://strbase.org). In this study only a fraction of the available data was gathered to assess whether sufficient ancestral information could be obtained to infer and individuals population group and to which level the assignment is accurate.…”

Section: Introductionmentioning

confidence: 99%

Implementing genotypic AmpFlSTR ® Identifiler ® Plus profiles to infer population groups

Ristow

Davison

D’Amato

2015

Forensic Science International: Genetics Supplement Series

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In this study Identifiler ® Plus was evaluated in its capacity to infer ancestry by comparing genotypic data garnered for several populations.Implementing pairwise F statistics (Fst) and an unsupervised Bayesian clustering method (STRUCTURE) significant genetic structure was observed between the African, European and Asian population groups. The Khoi-San group Ju\'hoansi showed the highest differentiation (Fst) with the non-African populations.High correct assignment rates were obtained using likelihood ratios with low error rates, this highlights the significant population structure found. A frequentist method was employed to identify Fst outliers and locus TH01 was shown to be under positive selective pressure.In this study a forensic kit for human identification has been shown to contain important ancestry information which may aid forensics case work if a sufficiently large reference database is established.

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PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile

Cited by 44 publications

References 39 publications

Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci

Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci

Genetic evidence for an East Asian origin of Chinese Muslim populations Dongxiang and Hui

Implementing genotypic AmpFlSTR ® Identifiler ® Plus profiles to infer population groups

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