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RETRACTED ARTICLE: Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs

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This article was retracted on 07 September 2021

This article has been updated

Abstract

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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Change history

  • 26 February 2020

    Editor's Note: Concerns have been raised about the ethics approval and informed consent procedures related to the research reported in this paper. The paper includes the following author declarations: “All subjects provided written informed content”. Editorial action will be taken as appropriate once an investigation of the concerns is complete and all parties have been given an opportunity to respond in full.

  • 07 September 2021

    This article has been retracted. Please see the Retraction Notice for more detail: https://doi.org/10.1007/s00414-021-02693-x

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Acknowledgments

Special thanks are given to Professor Kenneth. K. Kidd of Yale University who supplied cell line DNA samples.

Funding

This work was funded in part by the National Key Research and Development Program of China (2017YFC0803501) and the basic research project (2016JB039, 2017JB026, and 2016TGYDGAES14). Biological samples from the Caixia laboratory were funded by the National Infrastructure of Chinese Genetic Resources (NICGR:YCZYPT[2017]01-3) and the basic research project (2017JB025).

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Authors and Affiliations

Authors

Corresponding authors

Correspondence to Chao Liu, Hui-Jun Wang or Cai-Xia Li.

Ethics declarations

All subjects provided written informed content and self-declared ancestry information.

Additional information

Highlights

• A 28-AIM panel can distinguish five groups of population globally.

• With more samples, South Asia can be differentiated but has a lower PSD value than others.

• Likelihood ratio, ancestry components, and AMP (assignment match probability) were analyzed for individual ancestry assignment.

• The panel performed well on a test set of 663 individuals from 12 populations.

• It can be used for ancestry inference in forensic practice.

This article has been retracted. Please see the retraction notice for more detail: https://dx.doi.org/10.1007/s00414-021-02693-x

Electronic supplementary material

Supplemental Fig.1

Electropherogram of 28-plex-SNP genotypes obtained from the control DNA 9947. (PNG 120 kb)

High resolution image (TIF 838 kb)

Supplemental Fig. 2

Pairwise Fst of the 28 loci. (PNG 165 kb)

High resolution image (TIF 25518 kb)

Supplemental File 1

(Contains the results of DNA sequencing by Sangon Biotech Shanghai Co Ltd). (PDF 213 kb)

Supplemental Table 1

The information of PCR primers, the SBE primers, and the amplicons of the 28 loci. (XLSX 18 kb)

Supplemental Table 2

Table of the mean likelihood (L(K)) and variance for all of the K values. (XLSX 22 kb)

Supplemental Table 3

AMP and LR of the test samples. (XLSX 186 kb)

Supplemental Table 4

The ancestry component of the individuals. (XLSX 194 kb)

Supplemental Table 5

The summary of the allele detection rate of three analyses of the standard DNA 9947 at six concentrations. (DOC 36 kb)

Supplemental Table 6

The AMP and ancestry component of the 91, 94, and 100% profile completeness (based on experiments) of the 28 loci for 9947A and the 80% profile completeness (20% random removal of the profiles). (XLSX 13 kb)

Supplemental Table 7

PSD values of the 28-plex SNP for the reference populations. (XLSX 10 kb)

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Hao, WQ., Liu, J., Jiang, L. et al. RETRACTED ARTICLE: Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs. Int J Legal Med 133, 975–982 (2019). https://doi.org/10.1007/s00414-018-1863-z

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  • DOI: https://doi.org/10.1007/s00414-018-1863-z

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