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A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

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26 February 2020 ‘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: “Samples from all subjects were obtained with 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.’

Abstract

A single-tube multiplex assay of a small set of ancestry-informative markers (AIMs) for effectively estimating individual ancestry and admixture is an ideal forensic tool to trace the population origin of an unknown DNA sample. We present a newly developed 27-plex single nucleotide polymorphism (SNP) panel with highly robust and balanced differential power to perfectly assign individuals to African, European, and East Asian ancestries. Evaluating 968 previously described intercontinental AIMs from three HapMap population genotyping datasets (Yoruban in Ibadan, Nigeria (YRI); Utah residents with Northern and Western European ancestry from the Centre de'Etude du Polymorphism Humain (CEPH) collection (CEU); and Han Chinese in Beijing, China (CHB)), the best set of markers was selected on the basis of Hardy-Weinberg equilibrium (p > 0.00001), population-specific allele frequency (two of three δ values >0.5), according to linkage disequilibrium (r 2 < 0.2), and capable of being multiplexed in one tube and detected by capillary electrophoresis. The 27-SNP panel was first validated by assigning the ancestry of the 11 populations in the HapMap project. Then, we tested the 27-plex SNP assay with 1164 individuals from 17 additional populations. The results demonstrated that the SNP panel was successful for ancestry inference of individuals with African, European, and East Asian ancestry. Furthermore, the system performed well when inferring the admixture of Eurasians (EUR/EAS) after analyzing admixed populations from Xinjiang (Central Asian) as follows: Tajik (68:27), Uyghur (49:46), Kirgiz (40:57), and Kazak (36:60). For individual analyses, we interpreted each sample with a three-ancestry component percentage and a population match probability sequence. This multiplex assay is a convenient and cost-effective tool to assist in criminal investigations, as well as to correct for the effects of population stratification for case-control studies.

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  • 26 February 2020

    ‘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: “Samples from all subjects were obtained with 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.’

References

  1. Shriver MD, Smith MW, Jin L, Marcini A, Akey JM, Deka R, Ferrell RE (1997) Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet 60(4):957–964

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 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  PubMed  Google Scholar 

  3. Phillips C, Salas A, Sanchez JJ, Fondevila M, Gomez-Tato A, Alvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV, Carracedo A (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1(3–4):273–280. doi:10.1016/S1872-4973(07)00101-9

    Article  CAS  PubMed  Google Scholar 

  4. Kersbergen P, van Duijn K, Kloosterman AD, den Dunnen JT, Kayser M, de Knijff P (2009) Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans. BMC Genet 10:69. doi:10.1186/1471-2156-10-69

    Article  PubMed  PubMed Central  Google Scholar 

  5. Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, De La Vega FM, Seldin MF (2009) Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat 30(1):69–78. doi:10.1002/humu.20822

    Article  PubMed  PubMed Central  Google Scholar 

  6. 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. doi:10.1016/S1872-4973(14)00003-9

    Article  CAS  PubMed  Google Scholar 

  7. Qin P, Li Z, Jin W, Lu D, Lou H, Shen J, Jin L, Shi Y, Xu S (2014) A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese. Eur J Hum Genet 22(2):248–253. doi:10.1038/ejhg.2013.111

    Article  CAS  PubMed  Google Scholar 

  8. Galanter JM, Fernandez-Lopez JC, Gignoux CR, Barnholtz-Sloan J, Fernandez-Rozadilla C, Via M, Hidalgo-Miranda A, Contreras AV, Figueroa LU, Raska P, Jimenez-Sanchez G, Zolezzi IS, Torres M, Ponte CR, Ruiz Y, Salas A, Nguyen E, Eng C, Borjas L, Zabala W, Barreto G, Gonzalez FR, Ibarra A, Taboada P, Porras L, Moreno F, Bigham A, Gutierrez G, Brutsaert T, Leon-Velarde F, Moore LG, Vargas E, Cruz M, Escobedo J, Rodriguez-Santana J, Rodriguez-Cintron W, Chapela R, Ford JG, Bustamante C, Seminara D, Shriver M, Ziv E, Burchard EG, Haile R, Parra E, Carracedo A (2012) Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. PLoS Genet 8(3):e1002554. doi:10.1371/PGENETICS-D-11-02039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, Hirbo JB, Awomoyi AA, Bodo JM, Doumbo O, Ibrahim M, Juma AT, Kotze MJ, Lema G, Moore JH, Mortensen H, Nyambo TB, Omar SA, Powell K, Pretorius GS, Smith MW, Thera MA, Wambebe C, Weber JL, Williams SM (2009) The genetic structure and history of Africans and African Americans. Science 324(5930):1035–1044. doi:10.1126/science.1172257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Bigham A, Bauchet M, Pinto D, Mao X, Akey JM, Mei R, Scherer SW, Julian CG, Wilson MJ, Lopez Herraez D, Brutsaert T, Parra EJ, Moore LG, Shriver MD (2010) Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data. PLoS Genet 6(9):e1001116. doi:10.1371/journal.pgen.1001116

    Article  PubMed  PubMed Central  Google Scholar 

  11. Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB, Prchal JT, Ge R (2010) Genetic evidence for high-altitude adaptation in Tibet. Science 329(5987):72–75. doi:10.1126/science.1189406

    Article  CAS  PubMed  Google Scholar 

  12. Huerta-Sanchez E, Jin X, Asan BZ, Peter BM, Vinckenbosch N, Liang Y, Yi X, He M, Somel M, Ni P, Wang B, Ou X, Huasang LJ, Cuo ZX, Li K, Gao G, Yin Y, Wang W, Zhang X, Xu X, Yang H, Li Y, Wang J, Nielsen R (2014) Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512(7513):194–197. doi:10.1038/nature13408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Fondevila M, Phillips C, Santos C, Freire Aradas A, Vallone PM, Butler JM, Lareu MV, Carracedo A (2013) Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies. Forensic Sci Int Genet 7(1):63–74. doi:10.1016/S1872-4973(12)00140-8

    Article  CAS  PubMed  Google Scholar 

  14. Phillips C, Freire Aradas A, Kriegel AK, Fondevila M, Bulbul O, Santos C, Serrulla Rech F, Perez Carceles MD, Carracedo A, 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. doi:10.1016/S1872-4973(13)00059-8

    Article  CAS  PubMed  Google Scholar 

  15. Jia J, Wei YL, Qin CJ, Hu L, Wan LH, Li CX (2014) Developing a novel panel of genome-wide ancestry informative markers for bio-geographical ancestry estimates. Forensic Sci Int Genet 8(1):187–194. doi:10.1016/S1872-4973(13)00193-2

    Article  CAS  PubMed  Google Scholar 

  16. Epstein MP, Allen AS, Satten GA (2007) A simple and improved correction for population stratification in case–control studies. Am J Hum Genet 80(5):921–930. doi:10.1086/S0002-9297(07)60947-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. King TE, Parkin EJ, Swinfield G, Cruciani F, Scozzari R, Rosa A, Lim SK, Xue Y, Tyler-Smith C, Jobling MA (2007) Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogy. Eur J Hum Genet 15(3):288–293. doi:10.1038/sj.ejhg.5201771

    Article  CAS  PubMed  Google Scholar 

  18. Silva NM, Pereira L, Poloni ES, Currat M (2012) Human neutral genetic variation and forensic STR data. PLoS One 7(11):e49666. doi:10.1371/PONE-D-12-16962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Phillips C, Fernandez-Formoso L, Gelabert-Besada M, Garcia-Magarinos M, Santos C, Fondevila M, Carracedo A, Lareu MV (2013) Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing. Electrophoresis 34(8):1151–1162. doi:10.1002/elps.201200621

    Article  CAS  PubMed  Google Scholar 

  20. Halder I, Shriver M, Thomas M, Fernandez JR, Frudakis T (2008) A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications. Hum Mutat 29(5):648–658. doi:10.1002/humu.20695

    Article  CAS  PubMed  Google Scholar 

  21. Pemberton TJ, Wang C, Li JZ, Rosenberg NA (2010) Inference of unexpected genetic relatedness among individuals in HapMap Phase III. Am J Hum Genet 87(4):457–464. doi:10.1016/S0002-9297(10)00427-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Bouakaze C, Keyser C, Crubezy E, Montagnon D, Ludes B (2009) Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis. Int J Legal Med 123(4):315–325. doi:10.1007/s00414-009-0348-5

    Article  PubMed  Google Scholar 

  23. Walsh S, Liu F, Ballantyne KN, van Oven M, Lao O, Kayser M (2011) IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Sci Int Genet 5(3):170–180. doi:10.1016/S1872-4973(10)00032-3

    Article  CAS  PubMed  Google Scholar 

  24. Walsh S, Liu F, Wollstein A, Kovatsi L, Ralf A, Kosiniak-Kamysz A, Branicki W, Kayser M (2013) The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Sci Int Genet 7(1):98–115. doi:10.1016/S1872-4973(12)00181-0

    Article  CAS  PubMed  Google Scholar 

  25. Holsinger KE, Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet 10(9):639–650. doi:10.1038/nrg2611

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73(6):1402–1422. doi:10.1086/S0002-9297(07)63990-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Xu S, Jin L (2008) A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery. Am J Hum Genet 83(3):322–336. doi:10.1016/S0002-9297(08)00439-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575. doi:10.1086/S0002-9297(07)61352-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19(9):1655–1664. doi:10.1101/gr.094052.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164(4):1567–1587

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Rousset F (2008) genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8(1):103–106. doi:10.1111/j.1471-8286.2007.01931.x

    Article  PubMed  Google Scholar 

  33. Paschou P, Ziv E, Burchard EG, Choudhry S, Rodriguez-Cintron W, Mahoney MW, Drineas P (2007) PCA-correlated SNPs for structure identification in worldwide human populations. PLoS Genet 3(9):1672–1686

    Article  CAS  PubMed  Google Scholar 

  34. Phillips C, Parson W, Lundsberg B, Santos C, Freire-Aradas A, Torres M, Eduardoff M, Borsting C, Johansen P, Fondevila M, Morling N, Schneider P, 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. doi:10.1016/S1872-4973(14)00040-4

    Article  CAS  PubMed  Google Scholar 

  35. Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonne-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26(3):358–361. doi:10.1038/81685

    Article  CAS  PubMed  Google Scholar 

  36. O'Rourke DH, Raff JA (2010) The human genetic history of the Americas: the final frontier. Curr Biol 20(4):R202–R207. doi:10.1016/S0960-9822(09)02066-1

    Article  CAS  PubMed  Google Scholar 

  37. Wang CC, Li H (2013) Inferring human history in East Asia from Y chromosomes. Investig Genet 4(1):11. doi:10.1186/2041-2223-4-11

    Article  PubMed  PubMed Central  Google Scholar 

  38. Xu S, Huang W, Qian J, Jin L (2008) Analysis of genomic admixture in Uyghur and its implication in mapping strategy. Am J Hum Genet 82(4):883–894. doi:10.1016/S0002-9297(08)00166-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. 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. doi:10.1186/2041-2223-2-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Ovchinnikov IV, Malek MJ, Drees K, Kholina OI (2014) Mitochondrial DNA variation in Tajiks living in Tajikistan. Leg Med (Tokyo)

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Acknowledgments

This work was supported by a grant from the Key Projects in the National Science & Technology Pillar Program in the 12th-year Plan Period (no. 2012BAK02B01) and Basic Research Project (no. 2013JB018). The authors would like to thank Kenneth K. Kidd (Yale University), Bruce Budowle (University of North Texas), and Kiha Kim (Seoul National University) for providing population samples.

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Authors and Affiliations

  1. Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People’s Republic of China

    Yi-Liang Wei, Li Wei, Lei Zhao, Qi-Fan Sun, Li Jiang, Tao Zhang, Jian Ye, Lan Hu & Cai-Xia Li

  2. Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, 300070, Tianjin, People’s Republic of China

    Yi-Liang Wei

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

    Yi-Liang Wei, Lei Zhao, Qi-Fan Sun, Li Jiang, Tao Zhang, Jian Ye, Lan Hu & Cai-Xia Li

  4. Faculty of Forensic Sciences, Shanxi Medical University, Taiyuan, 030001, Shanxi, People’s Republic of China

    Li Wei

  5. Institution of Forensic Science of Bingtuan Public Security Bureau, Urumqi, 830000, Xinjiang, People’s Republic of China

    Hai-Bo Liu

  6. Xinjiang Public Security Department, Science and Technology Institute, Urumqi, 830006, Xinjiang, People’s Republic of China

    Jian-Gang Chen

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  1. Yi-Liang Wei
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Wei, YL., Wei, L., Zhao, L. et al. A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents. Int J Legal Med 130, 27–37 (2016). https://doi.org/10.1007/s00414-015-1183-5

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