Skip to main content
SpringerLink
Log in

Genetic structure and differentiation analysis of a Eurasian Uyghur population by use of 27 continental ancestry-informative SNPs

  • Original Article
  • Published:
International Journal of Legal Medicine Aims and scope Submit manuscript

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 consent and self-declared ancestry information. The study was approved by the Ethics Committee of the Institute of Forensic Science, Ministry of Public Security, People’s Republic of China, and the experiment was conducted according to the approved guidelines.” 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

Previously, we developed and validated a multiplex assay of 27 ancestry-informative markers (AIMs) for analyzing African (AFR), European (EUR), and East Asian (EAS) ancestry components. In this study, we typed and collectively analyzed a large Uyghur sample of 979 individuals to estimate the genetic coefficients of the 27 AIMs and investigate differentiation parameters between Uyghur and Han. The Uyghur allele frequencies ranged from 0.243 to 0.952, and heterozygosities ranged from 0.091 to 0.500. Values of F st3 and I n3 for EUR, Uyghur, and EAS ranged from 0.028 to 0.550 and 0.0002 to 0.345, respectively. The Uyghur population displays a substantial ancestry contribution of 50.3:49.7 (EUR:EAS) and was efficiently discriminated from Han Chinese with an accuracy of 99.285 %. All populations were clustered into AFR, EUR, EAS, and admixture groups of these three ancestries. Central Asian was obviously stratified from the other admixture populations of South Asians, North Asians, and the Americans. The 27 SNPs yield a circle with an average distance of 0.936 from the center (0, 0) in PCA analysis. Using this set, Chinese Uyghur and Han populations achieved accurate differentiation, and our updated genotype database (by citing 1000 Genomes data) of 43 worldwide populations is a useful resource for forensic applications and disease association studies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Change history

  • 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 consent and self-declared ancestry information. The study was approved by the Ethics Committee of the Institute of Forensic Science, Ministry of Public Security, People’s Republic of China, and the experiment was conducted according to the approved guidelines.” 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. Epstein MP, Allen AS, Satten GA (2007) A simple and improved correction for population stratification in case-control studies. Am J Hum Genet 80:921–930

    Article  CAS  Google Scholar 

  2. 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 324:1035–1044

    Article  CAS  Google Scholar 

  3. 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:e1001116

    Article  Google Scholar 

  4. Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73:1402–1422

    Article  CAS  Google Scholar 

  5. Phillips C (2015) Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet

  6. 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 29:648–658

    Article  CAS  Google Scholar 

  7. 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

    Article  Google Scholar 

  8. 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 30:69–78

    Article  Google Scholar 

  9. 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

    Article  CAS  Google Scholar 

  10. Kim JJ, Verdu P, Pakstis AJ, Speed WC, Kidd JR, Kidd KK (2005) Use of autosomal loci for clustering individuals and populations of East Asian origin. Hum Genet 117:511–519

    Article  Google Scholar 

  11. 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, Consortium L (2012) Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. PLoS Genet 8:e1002554

    Article  CAS  Google Scholar 

  12. Suo C, Xu H, Khor CC, Ong RT, Sim X, Chen J, Tay WT, Sim KS, Zeng YX, Zhang X, Liu J, Tai ES, Wong TY, Chia KS, Teo YY (2012) Natural positive selection and north-south genetic diversity in East Asia. Eur J Hum Genet 20:102–110

    Article  CAS  Google Scholar 

  13. Xu S, Yin X, Li S, Jin W, Lou H, Yang L, Gong X, Wang H, Shen Y, Pan X, He Y, Yang Y, Wang Y, Fu W, An Y, Wang J, Tan J, Qian J, Chen X, Zhang X, Sun Y, Zhang X, Wu B, Jin L (2009) Genomic dissection of population substructure of Han Chinese and its implication in association studies. Am J Hum Genet 85:762–774

    Article  CAS  Google Scholar 

  14. 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 22:248–253

    Article  CAS  Google Scholar 

  15. 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, Consortium SN (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1:273–280

    Article  CAS  Google Scholar 

  16. 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 7:359–366

    Article  CAS  Google Scholar 

  17. 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 8:187–194

    Article  CAS  Google Scholar 

  18. Rogalla U, Rychlicka E, Derenko MV, Malyarchuk BA, Grzybowski T (2015) Simple and cost-effective 14-loci SNP assay designed for differentiation of European East Asian and African samples. Forensic Sci Int Genet 14:42–49

    Article  CAS  Google Scholar 

  19. Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, Blue-Smith J, Jin L, Su B, Pitchappan R, Shanmugalakshmi S, Balakrishnan K, Read M, Pearson NM, Zerjal T, Webster MT, Zholoshvili I, Jamarjashvili E, Gambarov S, Nikbin B, Dostiev A, Aknazarov O, Zalloua P, Tsoy I, Kitaev M, Mirrakhimov M, Chariev A, Bodmer WF (2001) The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc Natl Acad Sci U S A 98:10244–10249

    Article  CAS  Google Scholar 

  20. Wei YL, Wei L, Zhao L, Sun QF, Jiang L, Zhang T, Liu HB, Chen JG, Ye J, Hu L, Li CX (2016) A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents. Int J Legal Med 130:27–37

    Article  Google Scholar 

  21. Yao YG, Kong QP, Wang CY, Zhu CL, Zhang YP (2004) Different matrilineal contributions to genetic structure of ethnic groups in the silk road region in china. Mol Biol Evol 21:2265–2280

    Article  CAS  Google Scholar 

  22. 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 82:883–894

    Article  CAS  Google Scholar 

  23. 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 83:322–336

    Article  CAS  Google Scholar 

  24. Smith MW, O'Brien SJ (2005) Mapping by admixture linkage disequilibrium: advances, limitations and guidelines. Nat Rev Genet 6:623–632

    Article  CAS  Google Scholar 

  25. Genomes Project C, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073

    Article  Google Scholar 

  26. Pemberton TJ, Wang C, Li JZ, Rosenberg NA (2010) Inference of unexpected genetic relatedness among individuals in HapMap Phase III. Am J Hum Genet 87:457–464

    Article  CAS  Google Scholar 

  27. 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 81:559–575

    Article  CAS  Google Scholar 

  28. 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 60:957–964

    CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  30. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181

    Article  CAS  Google Scholar 

  31. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322–1332

    Article  Google Scholar 

  32. Santos C, Phillips C, Oldoni F, Amigo J, Fondevila M, Pereira R, Carracedo A, Lareu MV (2015) Completion of a worldwide reference panel of samples for an ancestry informative Indel assay. Forensic Sci Int Genet 17:75–80

    Article  CAS  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 3:1672–1686

    Article  CAS  Google Scholar 

  34. Zeng X, Chakraborty R, King JL, LaRue B, Moura-Neto RS, Budowle B (2015) Selection of highly informative SNP markers for population affiliation of major US populations. Int J Legal Med

Download references

Acknowledgments

This work was supported by grants from the Key Projects in the National Science & Technology Pillar Program in the 12th year Plan Period (2012BAK02B01), the National Natural Science Foundation for Young Scholars of China (no. 81202384), and the Science and Technology Innovation Base Program of Beijing (no. Z141106004414084).

Author information

Author notes

    Authors and Affiliations

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

      Yi-Liang Wei, Qi-Fan Sun, Lei Zhao, Yuan Ou, 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, Tianjin, 300070, People’s Republic of China

      Yi-Liang Wei

    3. Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, People’s Republic of China

      Yi-Liang Wei

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

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

    5. Department of Nephrology, Tianjin TEDA Hospital, Tianjin, 300457, People’s Republic of China

      Qing Li

    6. Center Laboratory of Prenatal Diagnosis, Obstetrical, Tsingdao Municipal Hospital, Tsingdao, 266017, Shandong, People’s Republic of China

      Jun-Ling Yi

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

      Tao Zhang & Hai-Bo Liu

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

      Jian-Gang Chen

    9. Research Center of Stomatology, Stomatological Hospital, Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China

      Bo-Feng Zhu

    Authors
    1. Yi-Liang Wei
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Qi-Fan Sun
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Qing Li
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Jun-Ling Yi
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Lei Zhao
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Yuan Ou
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Li Jiang
      View author publications

      You can also search for this author in PubMed Google Scholar

    8. Tao Zhang
      View author publications

      You can also search for this author in PubMed Google Scholar

    9. Hai-Bo Liu
      View author publications

      You can also search for this author in PubMed Google Scholar

    10. Jian-Gang Chen
      View author publications

      You can also search for this author in PubMed Google Scholar

    11. Bo-Feng Zhu
      View author publications

      You can also search for this author in PubMed Google Scholar

    12. Jian Ye
      View author publications

      You can also search for this author in PubMed Google Scholar

    13. Lan Hu
      View author publications

      You can also search for this author in PubMed Google Scholar

    14. Cai-Xia Li
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding authors

    Correspondence to Yi-Liang Wei or Cai-Xia Li.

    Ethics declarations

    Samples from all subjects were obtained with written informed consent and self-declared ancestry information. The study was approved by the Ethics Committee of the Institute of Forensic Science, Ministry of Public Security, People’s Republic of China, and the experiment was conducted according to the approved guidelines.

    Additional information

    Yi-Liang Wei and Qi-Fan Sun contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Fig. S1

    (DOCX 221 kb)

    Fig. S2

    (DOCX 49 kb)

    Table S1

    (DOCX 17 kb)

    Table S2

    (DOCX 18 kb)

    Table S3

    (DOCX 14 kb)

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Wei, YL., Sun, QF., Li, Q. et al. Genetic structure and differentiation analysis of a Eurasian Uyghur population by use of 27 continental ancestry-informative SNPs. Int J Legal Med 130, 897–903 (2016). https://doi.org/10.1007/s00414-016-1335-2

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s00414-016-1335-2

    Keywords

    Search

    Navigation