[an error occurred while processing this directive]
Technique and Method

Optimization and validation of analysis method based on 27-plex SNP panel for ancestry inference

Expand
  • 1. Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
    2. Key Laboratory of Forensic Genetics, Ministry of Public Security, Beijing 100038, China

Received date: 2016-10-17

  Revised date: 2017-01-01

  Online published: 2017-01-12

Supported by

the National Science & Technology Pillar Program during the 12th Five-year Plan Period(2012BAK02B01);the Fundamental Research Funds for Institute of Forensic Science(2015JB023,2016JB039)

Abstract

Anthropology generally divides the individuals into the East Asian Mongolia race, European Caucasian race and African Nigro race. The 27-plex single nucleotide polymorphism (SNP) panel for ancestry information has been established to differentiate samples from East Asian, European, African and admixture populations of East Asian and European origin by genotyping and ancestry inference. To infer ancestry for unknown individuals, we established an optimized analysis pipeline based on the likelihood ratio, ancestry component and individual ancestry assignment. Four samples from East Asian, European, African and admixture populations of East Asian and European origin were tested using the optimized analysis pipeline. Cross validation within basic referential database and validation of 1 010 test samples were both used to evaluate the inference process. The results showed that accuracy of the method was higher than 99% in East Asia, Europe, Africa and admixture populations. The inference method can characterize the ancestry information of DNA donors, and has important practical application values in the field of human molecular and forensic genetics.

Cite this article

Li Jiang,Qifan Sun,Quan Ma,Wenting Zhao,Jing Liu,Lei Zhao,Anquan Ji,Caixia Li . Optimization and validation of analysis method based on 27-plex SNP panel for ancestry inference[J]. Hereditas(Beijing), 2017 , 39(2) : 166 -173 . DOI: 10.16288/j.yczz.16-346

References

[1] Zhang JZ. Forensic Anthropology. Beijing: People's Medical Publishing House, 2009.
[1] 张继宗. 法医人类学. 北京: 人民卫生出版社, 2009.
[2] Snow CC. Forensic anthropology. Springer US, 1982, 13(11): 49-67.
[3] 阿布都热合曼·阿布力米提, 陈开旭, 任志娟, 朱红娟, 单文娟, 张富春, 马正海, 郑秀芬. 新疆不同地区维吾尔族人群具有不同的遗传多样性—地域与遗传的关系. 见: 中国的遗传学研究——遗传学进步推动中国西部经济与社会发展——2011年中国遗传学会大会论文摘要汇编, 乌鲁木齐, 2011.
[4] Han KX. The ethnic anthropology of the ancient residents in Xinjiang and the constitutional characteristics of the Uygur nationality. Western Regions Stud, 1991, (2): 1-13, 131.
[4] 韩康信. 新疆古代居民的种族人类学研究和维吾尔族的体质特点. 西域研究, 1991, (2): 1-13, 131.
[5] Phillips C. Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet, 2015, 18: 49-65.
[6] Phillips C. Ancestry informative markers. Encycl Forensic Sci, 2013: 323-331, doi: 10.1016/B978-0-12-382165-2. 00060-X.
[7] Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang RX, Madbouly A, Maiers M, Middha M, Friedlaender FR, Kidd JR. Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet, 2014, 10: 23-32.
[8] Li CX, Pakstis AJ, Jiang L, Wei YL, Sun QF, Wu H, Bulbul O, Wang P, Kang LL, Kidd JR, Kidd KK. A panel of 74 AISNPs: improved ancestry inference within Eastern Asia. Forensic Sci Int Genet, 2016, 23: 101-110.
[9] Santos C, Fondevila M, Ballard D, Banemann R, Bento AM, B?rsting 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, van Oorschot RAH, Zatkalikova L, Carracedoá, Phillips C. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: results of a collaborative EDNAP exercise. Forensic Sci Int Genet, 2015, 19: 56-67.
[10] Wei YL, Wei L, Zhao L, Sun QF, Jiang L, Zhang T, Liu HB, Chen JG, Ye J, Hu L, Li CX. A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents. Int J Legal Med, 2016, 130(1): 27-37.
[11] Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, álvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV, Carracedoa á. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Geneti, 2008, 1(3-4): 273-280.
[12] Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK. Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 p
Outlines

/