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RETRACTED ARTICLE: Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs

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International Journal of Legal Medicine Aims and scope Submit manuscript

This article was retracted on 07 September 2021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

References

  1. Santos C, Fondevila M, Ballard D, Banemann R, Bento AM, Børsting C, Branicki W, Brisighelli F, Burrington M, Capal T, Chaitanya L, Daniel R, Decroyer V, England R, Gettings KB, Gross TE, Haas C, Harteveld J, Hoff-Olsen P, Hoffmann A, Kayser M, Kohler P, Linacre A, Mayr-Eduardoff M, McGovern C, Morling N, O'Donnell G, Parson W, Pascali VL, Porto MJ, Roseth A, Schneider PM, Sijen T, Stenzl V, Court DS, Templeton JE, Turanska M, Vallone PM, Oorschot RAHV, Zatkalikova L, Carracedo Á, Phillips C, EUROFORGEN-NoE Consortium (2015) Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: results of a collaborative EDNAP exercise. Forensic Sci Int Genet 19:56–67

    Article  CAS  Google Scholar 

  2. Cho S, Yu HJ, Han J, Kim Y, Lee J, Lee SD (2014) Forensic application of SNP-based resequencing array for individual identification. Forensic Sci Int Genet 13:45–52

    Article  CAS  Google Scholar 

  3. Borsting C, Mogensen HS, Morling N (2013) Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples. Forensic Sci Int Genet 7(3):345–352

    Article  Google Scholar 

  4. Wei YL, Li CX, Jia J, Hu L, Liu Y (2012) Forensic identification using a multiplex assay of 47 SNPs. J Forensic Sci 57(6):1448–1456

    Article  CAS  Google Scholar 

  5. Li CX, Pakstis AJ, Jiang L, Wei YL, Sun QF, Wu H, Bulbul O, Wang P, Kang LL, Kidd JR, Kidd KK (2016) A panel of 74 AISNPs: improved ancestry inference within Eastern Asia. Forensic Sci Int Genet 23:101–110

    Article  CAS  Google Scholar 

  6. Pakstis AJ, Haigh E, Cherni L, ElGaaied ABA, Barton A, Evsanaa B, Togtokh A, Brissenden J, Roscoe J, Bulbul O, Filoglu G, Gurkan C, Meiklejohn KA, Robertson JM, Li CX, Wei YL, Li H, Soundararajan U, Rajeevan H, Kidd JR, Kidd KK (2015) 52 additional reference population samples for the 55 AISNP panel. Forensic Sci Int Genet 19:269–271

    Article  CAS  Google Scholar 

  7. Phillips C, Fondevila M, Lareau MV (2012) A 34-plex autosomal SNP single base extension assay for ancestry investigations. Methods Mol Biol 830:109–126

    Article  CAS  Google Scholar 

  8. Inagaki S, Yamamoto Y, Doi Y, Takata T, Ishikawa T, Imabayashi K, Yoshitome K, Miyaishi S, Ishizu H (2004) A new 39-plex analysis method for SNPs including 15 blood group loci. Forensic Sci Int 144(1):45–57

    Article  CAS  Google Scholar 

  9. Wei Y et al (2016) A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents. Int J Legal Med 130(1):27–37

    Article  Google Scholar 

  10. Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, de la Vega FM, Kidd KK (2011) Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples. Investig Genet 2(1):1

    Article  CAS  Google Scholar 

  11. Phillips C, Parson W, Lundsberg B, Santos C, Freire-Aradas A, Torres M, Eduardoff M, Børsting C, Johansen P, Fondevila M, Morling N, Schneider P, EUROFORGEN-NoE Consortium, Carracedo A, Lareu MV (2014) Building a forensic ancestry panel from the ground up: the EUROFORGEN Global AIM-SNP set. Forensic Sci Int Genet 11:13–25

    Article  CAS  Google Scholar 

  12. Galanter JM et al (2012) Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. PLoS Genet 8(3):e1002554

    Article  CAS  Google Scholar 

  13. de la Puente M, Santos C, Fondevila M, Manzo L, EUROFORGEN-NoE Consortium, Carracedo Á, Lareu MV, Phillips C (2016) The Global AIMs Nano set: a 31-plex SNaPshot assay of ancestry-informative SNPs. Forensic Sci Int Genet 22:81–88

    Article  Google Scholar 

  14. Wei YL, Qin CJ, Liu HB, Jia J, Hu L, Li CX (2014) Validation of 58 autosomal individual identification SNPs in three Chinese populations. Croat Med J 55(1):10–13

    Article  CAS  Google Scholar 

  15. Frudakis T, Venkateswarlu K, Thomas MJ, Gaskin Z, Ginjupalli S, Gunturi S, Ponnuswamy V, Natarajan S, Nachimuthu PK (2003) A classifier for the SNP-based inference of ancestry. J Forensic Sci 48(4):771–782

    Article  CAS  Google Scholar 

  16. Budowle B, van Daal A (2008) Forensically relevant SNP classes. Biotechniques 44(5):603–608 610

    Article  CAS  Google Scholar 

  17. Sanchez JJ, Phillips C, Børsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27(9):1713–1724

    Article  CAS  Google Scholar 

  18. Kidd KK, Pakstis AJ, Speed WC, Grigorenko EL, Kajuna SLB, Karoma NJ, Kungulilo S, Kim JJ, Lu RB, Odunsi A, Okonofua F, Parnas J, Schulz LO, Zhukova OV, Kidd JR (2006) Developing a SNP panel for forensic identification of individuals. Forensic Sci Int 164(1):20–32

    Article  CAS  Google Scholar 

  19. Porras-Hurtado L et al (2013) An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet 4:98

    Article  Google Scholar 

  20. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  21. Rosenberg NA (2004) DISTRUCT a program for the graphical display of population structure. Mol Ecol Notes 4(1):137–138

    Article  Google Scholar 

  22. Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Alvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV, Carracedo A, SNPforID Consortium (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1(3–4):273–280

    Article  CAS  Google Scholar 

  23. Yang L, Tan SJ, Yu HJ, Zheng BR, Qiao EF, Dong YL, Zan RG, Xiao CJ (2008) Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism. Sci China C Life Sci 51(5):435–444

    Article  CAS  Google Scholar 

  24. Ballantyne KN, van Oven M, Ralf A, Stoneking M, Mitchell RJ, van Oorschot RAH, Kayser M (2012) MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Sci Int Genet 6(4):425–436

    Article  CAS  Google Scholar 

  25. Shi W, Ayub Q, Vermeulen M, Shao RG, Zuniga S, van der Gaag K, de Knijff P, Kayser M, Xue Y, Tyler-Smith C (2010) A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations. Mol Biol Evol 27(2):385–393

    Article  CAS  Google Scholar 

  26. Kayser M (2017) Forensic use of Y-chromosome DNA: a general overview. Hum Genet 136:621–635

    Article  CAS  Google Scholar 

  27. Pereira R, Phillips C, Pinto N, Santos C, Santos SEB, Amorim A, Carracedo Á, Gusmão L (2012) Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS One 7(1):e29684

    Article  CAS  Google Scholar 

  28. Phillips C, Aradas AF, Kriegel AK, Fondevila M, Bulbul O, Santos C, Rech FS, Carceles MDP, Carracedo Á, Schneider PM, Lareu MV (2013) Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries. Forensic Sci Int Genet 7(3):359–366

    Article  CAS  Google Scholar 

  29. Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A, Maiers M, Middha M, Friedlaender FR, Kidd JR (2014) Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet 10:23–32

    Article  CAS  Google Scholar 

  30. Ovchinnikov IV, Malek MJ, Drees K, Kholina OI (2014) Mitochondrial DNA variation in Tajiks living in Tajikistan. Legal Med (Tokyo) 16(6):390–395

    Article  CAS  Google Scholar 

  31. Triki-Fendri S, Sánchez-Diz P, Rey-González D, Alfadhli S, Ayadi I, Ben Marzoug R, Carracedo Á, Rebai A (2016) Genetic structure of the Kuwaiti population revealed by paternal lineages. Am J Hum Biol 28(2):203–212

    Article  Google Scholar 

  32. Phillips C (2015) Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet 18:49–65

    Article  CAS  Google Scholar 

Download references

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).

Author information

Author notes

  1. Wei-Qi Hao and Jing Liu contributed equally to this work.

Authors and Affiliations

  1. Institute of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China

    Wei-Qi Hao, Chao Liu & Hui-Jun Wang

  2. Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People’s Republic of China

    Wei-Qi Hao, Jing Liu, Li Jiang, Jun-Ping Han, Ling Wang, Jiu-Ling Li, Quan Ma & Cai-Xia Li

  3. Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau, Beijing, 100102, China

    Jun-Ping Han

  4. Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, Guangdong, China

    Chao Liu

Authors
  1. Wei-Qi Hao
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  2. Jing Liu
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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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