Analysis of Uyghur and Kazakh populations using the Precision ID Ancestry Panel

H Simayijiang; C Børsting; T Tvedebrink; N Morling

doi:10.1016/j.fsigen.2019.102144

Analysis of Uyghur and Kazakh populations using the Precision ID Ancestry Panel

H Simayijiang, C Børsting, T Tvedebrink, N Morling

Research output: Contribution to journal › Journal article › Research › peer-review

13 Citations (Scopus)

Abstract

Autosomal ancestry informative markers (AIMs) are important markers for inferring ancestry of humans. In the present study, we typed 105 Uyghurs and 94 Kazakhs with the Precision ID Ancestry Panel that amplifies 165 autosomal AIMs. No statistically significant deviation from Hardy-Weinberg equilibrium and no linkage disequilibrium between loci was observed after Bonferroni correction. STRUCTURE and PCA analyses showed that Uyghurs and Kazakhs appeared as admixed individuals of primarily European and East Asian ancestry and were clearly differentiated from Europeans, Middle Easterners, South/Central Asians, and East Asians. However, it was not possible to differentiate the two populations from each other and they were also difficult to differentiate from Greenlanders, a population with European/Inuit admixture. GenoGeographer was used to evaluate the weight of the evidence. Initially, the results showed that the majority of AIM profiles from Uyghur and Kazakh individuals were not represented by any of the 36 reference populations of the GenoGeographer database. Consequently, it was not reasonable to infer the ancestry of these individuals. A randomly selected subset of the studied populations (75 Uyghur and 75 Kazakh individuals) was used to construct two new reference populations for GenoGeographer, and ancestry prediction was performed on the remaining test individuals. A total of 42 out of 49 test individuals were represented by at least one population after the introduction of Uyghur and Kazakh reference populations. Likelihood ratios ≥106 were obtained when the alternative hypothesis was that the individual belonged to the South/Central Asian, East Asian, Middle Eastern, European, or the admixed Greenlandic population.

Original language	English
Article number	102144
Journal	Forensic Science International: Genetics
Volume	43
ISSN	1872-4973
DOIs	https://doi.org/10.1016/j.fsigen.2019.102144
Publication status	Published - Nov 2019

Bibliographical note

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/locate/withdrawalpolicy).

This article has been retracted at the request of the Editor-in-Chief and Associate Editors of the journal after a thorough investigation.

It has come to light that the studies of the samples collected and used for this research are not covered by the approval H-3-2012-023 of the Danish Ethical Committee referred to in this paper. All authors have been informed of this decision. Apologies are offered to readers of the journal that this was not detected during the submission process.

Keywords

Ancestry informative markers
GenoGeographer
Kazakh
Massively parallel sequencing
Precision ID Ancestry Panel
Uyghur
Xinjiang
Genetics, Population
DNA Fingerprinting
Gene Frequency
Humans
Sequence Analysis, DNA
Linkage Disequilibrium
Ethnic Groups/genetics
Polymerase Chain Reaction
High-Throughput Nucleotide Sequencing
Polymorphism, Single Nucleotide
Principal Component Analysis

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@article{a6f17100aa4849048576d26ff4763189,

title = "Analysis of Uyghur and Kazakh populations using the Precision ID Ancestry Panel",

abstract = "Autosomal ancestry informative markers (AIMs) are important markers for inferring ancestry of humans. In the present study, we typed 105 Uyghurs and 94 Kazakhs with the Precision ID Ancestry Panel that amplifies 165 autosomal AIMs. No statistically significant deviation from Hardy-Weinberg equilibrium and no linkage disequilibrium between loci was observed after Bonferroni correction. STRUCTURE and PCA analyses showed that Uyghurs and Kazakhs appeared as admixed individuals of primarily European and East Asian ancestry and were clearly differentiated from Europeans, Middle Easterners, South/Central Asians, and East Asians. However, it was not possible to differentiate the two populations from each other and they were also difficult to differentiate from Greenlanders, a population with European/Inuit admixture. GenoGeographer was used to evaluate the weight of the evidence. Initially, the results showed that the majority of AIM profiles from Uyghur and Kazakh individuals were not represented by any of the 36 reference populations of the GenoGeographer database. Consequently, it was not reasonable to infer the ancestry of these individuals. A randomly selected subset of the studied populations (75 Uyghur and 75 Kazakh individuals) was used to construct two new reference populations for GenoGeographer, and ancestry prediction was performed on the remaining test individuals. A total of 42 out of 49 test individuals were represented by at least one population after the introduction of Uyghur and Kazakh reference populations. Likelihood ratios ≥106 were obtained when the alternative hypothesis was that the individual belonged to the South/Central Asian, East Asian, Middle Eastern, European, or the admixed Greenlandic population.",

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author = "H Simayijiang and C B{\o}rsting and T Tvedebrink and N Morling",

note = "This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief and Associate Editors of the journal after a thorough investigation. It has come to light that the studies of the samples collected and used for this research are not covered by the approval H-3-2012-023 of the Danish Ethical Committee referred to in this paper. All authors have been informed of this decision. Apologies are offered to readers of the journal that this was not detected during the submission process.",

year = "2019",

month = nov,

doi = "10.1016/j.fsigen.2019.102144",

language = "English",

volume = "43",

journal = "Forensic Science International: Genetics",

issn = "1872-4973",

publisher = "Elsevier",

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AU - Simayijiang, H

AU - Børsting, C

AU - Tvedebrink, T

AU - Morling, N

N1 - This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief and Associate Editors of the journal after a thorough investigation. It has come to light that the studies of the samples collected and used for this research are not covered by the approval H-3-2012-023 of the Danish Ethical Committee referred to in this paper. All authors have been informed of this decision. Apologies are offered to readers of the journal that this was not detected during the submission process.

PY - 2019/11

Y1 - 2019/11

N2 - Autosomal ancestry informative markers (AIMs) are important markers for inferring ancestry of humans. In the present study, we typed 105 Uyghurs and 94 Kazakhs with the Precision ID Ancestry Panel that amplifies 165 autosomal AIMs. No statistically significant deviation from Hardy-Weinberg equilibrium and no linkage disequilibrium between loci was observed after Bonferroni correction. STRUCTURE and PCA analyses showed that Uyghurs and Kazakhs appeared as admixed individuals of primarily European and East Asian ancestry and were clearly differentiated from Europeans, Middle Easterners, South/Central Asians, and East Asians. However, it was not possible to differentiate the two populations from each other and they were also difficult to differentiate from Greenlanders, a population with European/Inuit admixture. GenoGeographer was used to evaluate the weight of the evidence. Initially, the results showed that the majority of AIM profiles from Uyghur and Kazakh individuals were not represented by any of the 36 reference populations of the GenoGeographer database. Consequently, it was not reasonable to infer the ancestry of these individuals. A randomly selected subset of the studied populations (75 Uyghur and 75 Kazakh individuals) was used to construct two new reference populations for GenoGeographer, and ancestry prediction was performed on the remaining test individuals. A total of 42 out of 49 test individuals were represented by at least one population after the introduction of Uyghur and Kazakh reference populations. Likelihood ratios ≥106 were obtained when the alternative hypothesis was that the individual belonged to the South/Central Asian, East Asian, Middle Eastern, European, or the admixed Greenlandic population.

AB - Autosomal ancestry informative markers (AIMs) are important markers for inferring ancestry of humans. In the present study, we typed 105 Uyghurs and 94 Kazakhs with the Precision ID Ancestry Panel that amplifies 165 autosomal AIMs. No statistically significant deviation from Hardy-Weinberg equilibrium and no linkage disequilibrium between loci was observed after Bonferroni correction. STRUCTURE and PCA analyses showed that Uyghurs and Kazakhs appeared as admixed individuals of primarily European and East Asian ancestry and were clearly differentiated from Europeans, Middle Easterners, South/Central Asians, and East Asians. However, it was not possible to differentiate the two populations from each other and they were also difficult to differentiate from Greenlanders, a population with European/Inuit admixture. GenoGeographer was used to evaluate the weight of the evidence. Initially, the results showed that the majority of AIM profiles from Uyghur and Kazakh individuals were not represented by any of the 36 reference populations of the GenoGeographer database. Consequently, it was not reasonable to infer the ancestry of these individuals. A randomly selected subset of the studied populations (75 Uyghur and 75 Kazakh individuals) was used to construct two new reference populations for GenoGeographer, and ancestry prediction was performed on the remaining test individuals. A total of 42 out of 49 test individuals were represented by at least one population after the introduction of Uyghur and Kazakh reference populations. Likelihood ratios ≥106 were obtained when the alternative hypothesis was that the individual belonged to the South/Central Asian, East Asian, Middle Eastern, European, or the admixed Greenlandic population.

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KW - DNA Fingerprinting

KW - Gene Frequency

KW - Humans

KW - Sequence Analysis, DNA

KW - Linkage Disequilibrium

KW - Ethnic Groups/genetics

KW - Polymerase Chain Reaction

KW - High-Throughput Nucleotide Sequencing

KW - Polymorphism, Single Nucleotide

KW - Principal Component Analysis

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DO - 10.1016/j.fsigen.2019.102144

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SN - 1872-4973

VL - 43

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

M1 - 102144

ER -

Analysis of Uyghur and Kazakh populations using the Precision ID Ancestry Panel

Abstract

Bibliographical note

Keywords

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Retraction notice to “Analysis of Uyghur and Kazakh populations using the Precision ID Ancestry Panel” [Forensic Sci. Int. Genet. 43 (2019) 102144](S1872497319300419)(10.1016/j.fsigen.2019.102144)

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