技术与方法

27-plex SNP种族推断方法的优化及验证

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  • 1. 公安部物证鉴定中心,北京市现场物证检验工程技术研究中心,北京100038
    2. 法医遗传学公安部重点实验室,北京100038
江丽,博士,主检法医师,研究方向:法医遗传学。E-mail: jl@mail.bnu.edu.cn|李彩霞,博士,主任法医师,研究方向:法医遗传学。E-mail: licaixia@tsinghua.org.cn

收稿日期: 2016-10-17

  修回日期: 2017-01-01

  网络出版日期: 2017-01-12

基金资助

“十二五”国家科技支撑计划课题(2012BAK02B01);公安部物证鉴定中心基本科研业务费专项资金项目(2015JB023,2016JB039)

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

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  • 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)

摘要

人类学中常将人群分为东亚黄种人、欧洲白种人和非洲黑种人。27-plex SNP种族推断体系可针对来自东亚、欧洲、非洲及欧亚混合人群的样本进行分型检测进而推断其祖先来源。本研究对该体系获取样本分型后的种族推断分析方法进行了进一步优化,建立了一种基于似然比、祖先成分和种族归类的推断分析方法,并对4个来自东亚、欧洲、非洲及其混合人群的测试样本进行种族来源推断。使用基础参考数据库交叉验证和1010份测试样本验证两种方式进行了种族推断方法流程的评估研究。验证结果表明该方法体系在东亚、欧洲、非洲及欧亚混合人群中的推断准确性均高于99%。本种族推断方法可对DNA来源人的种族信息进行刻画,在人类分子遗传学、法医遗传学等领域有重要的应用价值。

本文引用格式

江丽,孙启凡,马泉,赵雯婷,刘京,赵蕾,季安全,李彩霞 . 27-plex SNP种族推断方法的优化及验证[J]. 遗传, 2017 , 39(2) : 166 -173 . DOI: 10.16288/j.yczz.16-346

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.

参考文献

[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
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