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

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• 作者：Yi-Liang Wei ; Li Wei ; Lei Zhao ; Qi-Fan Sun…
• 关键词：Ancestry ; informative markers ; Population structure ; Ancestry inference ; Multiplex assay
• 刊名：International Journal of Legal Medicine
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：130
• 期：1
• 页码：27-37
• 全文大小：1,064 KB
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• 作者单位：Yi-Liang Wei (1) (2) (3)
  Li Wei (1) (4)
  Lei Zhao (1) (3)
  Qi-Fan Sun (1) (3)
  Li Jiang (1) (3)
  Tao Zhang (1) (3)
  Hai-Bo Liu (5)
  Jian-Gang Chen (6)
  Jian Ye (1) (3)
  Lan Hu (1) (3)
  Cai-Xia Li (1) (3)
  
  1. Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People’s Republic of China
  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
  3. Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People’s Republic of China
  4. Faculty of Forensic Sciences, Shanxi Medical University, Taiyuan, 030001, Shanxi, People’s Republic of China
  5. Institution of Forensic Science of Bingtuan Public Security Bureau, Urumqi, 830000, Xinjiang, People’s Republic of China
  6. Xinjiang Public Security Department, Science and Technology Institute, Urumqi, 830006, Xinjiang, People’s Republic of China
  
• 刊物类别：Medicine
• 刊物主题：Medicine & Public Health
  Forensic Medicine
  Medical Law
  Medicine/Public Health, general
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1437-1596

文摘

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. Keywords Ancestry-informative markers Population structure Ancestry inference Multiplex assay