Establishing a second-tier panel of 18 ancestry informative markers to improve ancestry distinctions among Asian populations

Qu, Shengqiu; Zhu, Jing; Wang, Yinji; Yin, Lu; Lv, Meili; Wang, Li; Jian, Hui; Yu, Tao; Zhang, Ranran; Liu, Yuqing; Li, Fēi; Huang, Sicheng; Liang, Weibo; Zhang, Lin

doi:10.1016/j.fsigen.2019.05.001

Cited by 14 publications

(9 citation statements)

References 36 publications

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“…Qu et al. [14] reported a correct rate of 64% (144/225) be achieved using a second‐tier panel of 18 AISNPs. Comparing with the Snipper results of two target Asian AIMs panels mentioned above, our 21 AI‐InDels panel showed an improvement of inference correct rate in Chinese groups.…”

Section: Discussionmentioning

confidence: 99%

“…Subsequent research on the intracontinent biogeographic ancestry inference have been performed tentatively. Some AIMs panels developed with SNPs have been proved to reach a relative reliable performance of differentiating intracontinental subgroups [13, 14]. Few AI‐InDels panel was developed in biogeographic ancestry inference at intracontinental level.…”

Section: Introductionmentioning

confidence: 99%

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A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

et al. 2021

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CE is the primary methodology used in forensic DNA typing. Alleles of commonly used types of genetic markers could be separated and detected via CE based on dye color and migration time. Insertion/deletion (InDel) is an ideal genetic marker for forensic DNA analysis due to their abundance in the human genome, low mutation rate, availability of their allele types via CE, and elimination of stutter peaks. Moreover, InDels could be used as ancestry informative markers since allele frequencies of InDels is different among geographically separated populations. Several ancestry informative insertion/deletion panels have been established based on CE platform to achieve the intercontinental populations distinction. However, improvements to differentiate intracontinental populations is few. In this study, 21 InDels with fixation index (FST) > 0.15 were selected and assembled into one ancestry informative insertion/deletion panel. Using well‐designed primers, those 21 InDels could be amplified successfully and genotyped on the CE platform accurately and completely. The panel showed a large FST distance distinction among the ten Asian populations. Using clustering analysis, ten Asian populations were classified into three subgroups: East Asian, Southeast Asian, and South Asian subgroups. To evaluate the panel's capability in ancestry inference, a validation experiment was undertaken with 319 individuals from four geographically separated populations in China. Four Chinese populations were classified into different ancestry subgroups and 81.8% test individuals’ ancestry could be inferred correctly. Our result showed that development of high ancestry informative InDels panel based on CE platform is a potential for individual ancestry inference among intracontinental populations.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

et al. 2021

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“…The microhaplotype was firstly proposed by Kidd et al in 2013 [1]. It combines the advantages of STRs and SNPs, so it has attracted the attention of many researchers in the past few years [2,[21][22][23][24][25]. Among them, the SNP-SNP microhaplotype composed of two linked SNPs indicates a good potential for forensic practice.…”

Section: Discussionmentioning

confidence: 99%

A new approach to detect a set of SNP‐SNP markers: Combining ARMS‐PCR with SNaPshot technology

Zhang

Jian

et al. 2020

Electrophoresis

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Microhaplotypes are a new promising type of forensic genetic marker. Without the interference of stutter and high mutation rates as for STRs, and with short amplification lengths and a higher degree of polymorphism than single SNP, microhaplotypes composed of two SNPs, SNP-SNP, have a strong application potential. Currently, the most common method to detect microhaplotypes is massive parallel sequencing. However, the cost and extensive use of instruments limit its wide application in forensic laboratories. In this study, we screened 23 new SNP-SNP loci and established a new detection method by combining a multiplex amplification refractory mutation system-based PCR (ARMS-PCR) and SNaPshot technology based on CE. First, we introduced an additional deliberate mismatch at the antepenultimate base from the 3 end of primers when designing ARMS-PCR for SNP 1 (the first SNP of the SNP-SNP). Then, single base extension primers for SNaPshot assay were designed next to the position of SNP 2 (the second SNP). Finally, 15 loci were successfully built into four panels and these loci showed a relatively high level of polymorphism in the Southwest Chinese Han population. All the loci had an average probability of informative genotypes (I value) of 0.319 and a combined discrimination power of 0.999999999. Therefore, this new detection system will provide a valuable supplement to current methods.

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“…The best way to assign an individual into a particular population via genetic testing is to use ancestry informative markers (AIMs) –markers characterized by essential differences in allele frequencies between populations 3 – 5 . As proposed by several studies (for example 6 – 25 ), short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (InDels), and microhaplotypes can be used as AIMs for ancestry inference. However, autosomal single nucleotide polymorphisms are the best choices due to their inherent stability, high density of genome-wide distribution, and pronounced frequency variation among populations.…”

Section: Introductionmentioning

confidence: 99%

Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field

Alladio

Poggiali

Cosenza

et al. 2022

Sci Rep

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The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring their genealogy, and the capability to distinguish biogeographic information about population groups and subgroups via DNA analysis plays an essential role in several fields such as in forensics. In fact, for investigative and intelligence purposes, it is beneficial to inference the biogeographical origins of perpetrators of crimes or victims of unsolved cold cases when no reference profile from perpetrators or database hits for comparative purposes are available. Current approaches for biogeographical ancestry estimation using SNPs data are usually based on PCA and Structure software. The present study provides an alternative method that involves multivariate data analysis and machine learning strategies to evaluate BGA discriminating power of unknown samples using different commercial panels. Starting from 1000 Genomes project, Simons Genome Diversity Project and Human Genome Diversity Project datasets involving African, American, Asian, European and Oceania individuals, and moving towards further and more geographically restricted populations, powerful multivariate techniques such as Partial Least Squares-Discriminant Analysis (PLS-DA) and machine learning techniques such as XGBoost were employed, and their discriminating power was compared. PLS-DA method provided more robust classifications than XGBoost method, showing that the adopted approach might be an interesting tool for forensic experts to infer BGA information from the DNA profile of unknown individuals, but also highlighting that the commercial forensic panels could be inadequate to discriminate populations at intra-continental level.

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Establishing a second-tier panel of 18 ancestry informative markers to improve ancestry distinctions among Asian populations

Cited by 14 publications

References 36 publications

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

A new approach to detect a set of SNP‐SNP markers: Combining ARMS‐PCR with SNaPshot technology

Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field

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