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International Journal of Legal Medicine

, Volume 133, Issue 4, pp 975–982 | Cite as

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

  • Wei-Qi Hao
  • Jing Liu
  • Li Jiang
  • Jun-Ping Han
  • Ling Wang
  • Jiu-Ling Li
  • Quan Ma
  • Chao LiuEmail author
  • Hui-Jun WangEmail author
  • Cai-Xia LiEmail author
Short Communication

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.

Keywords

Forensic genetics AIMs Compound amplification Genetics structure analysis 

Notes

Acknowledgments

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

Funding information

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).

Compliance with ethical standards

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

Supplementary material

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Supplemental Fig.1

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

414_2018_1863_MOESM1_ESM.tif (839 kb)
High resolution image (TIF 838 kb)
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Supplemental Fig. 2

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

414_2018_1863_MOESM2_ESM.tif (24.9 mb)
High resolution image (TIF 25518 kb)
414_2018_1863_MOESM3_ESM.pdf (213 kb)
Supplemental File 1 (Contains the results of DNA sequencing by Sangon Biotech Shanghai Co Ltd). (PDF 213 kb)
414_2018_1863_MOESM4_ESM.xlsx (19 kb)
Supplemental Table 1 The information of PCR primers, the SBE primers, and the amplicons of the 28 loci. (XLSX 18 kb)
414_2018_1863_MOESM5_ESM.xlsx (22 kb)
Supplemental Table 2 Table of the mean likelihood (L(K)) and variance for all of the K values. (XLSX 22 kb)
414_2018_1863_MOESM6_ESM.xlsx (187 kb)
Supplemental Table 3 AMP and LR of the test samples. (XLSX 186 kb)
414_2018_1863_MOESM7_ESM.xlsx (194 kb)
Supplemental Table 4 The ancestry component of the individuals. (XLSX 194 kb)
414_2018_1863_MOESM8_ESM.doc (36 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)
414_2018_1863_MOESM9_ESM.xlsx (14 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)
414_2018_1863_MOESM10_ESM.xlsx (11 kb)
Supplemental Table 7 PSD values of the 28-plex SNP for the reference populations. (XLSX 10 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute of Forensic MedicineSouthern Medical UniversityGuangzhouChina
  2. 2.Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic ScienceInstitute of Forensic ScienceBeijingPeople’s Republic of China
  3. 3.Technology Department of Chaoyang Sub-bureauBeijing Public Security BureauBeijingChina
  4. 4.Guangdong Province Key Laboratory of Forensic GeneticsGuangzhou Forensic Science InstituteGuangzhouChina

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