title: A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents.
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.
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China. yiliangwei@yahoo.com.|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. yiliangwei@yahoo.com.|Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People's Republic of China. yiliangwei@yahoo.com.
authors.forename: Yi-Liang
authors.initials: YL
authors.lastname: Wei
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China.|Faculty of Forensic Sciences, Shanxi Medical University, Taiyuan, 030001, Shanxi, People's Republic of China.
authors.forename: Li
authors.initials: L
authors.lastname: Wei
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China.|Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China.|Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People's Republic of China.
authors.forename: Qi-Fan
authors.initials: QF
authors.lastname: Sun
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China.|Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People's Republic of China.
authors.forename: Li
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China.|Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Institution of Forensic Science of Bingtuan Public Security Bureau, Urumqi, 830000, Xinjiang, People's Republic of China.
authors.forename: Hai-Bo
authors.initials: HB
authors.lastname: Liu
authors.affiliation: Xinjiang Public Security Department, Science and Technology Institute, Urumqi, 830006, Xinjiang, People's Republic of China.
authors.forename: Jian-Gang
authors.initials: JG
authors.lastname: Chen
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China.|Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People's Republic of China.
authors.forename: Jian
authors.initials: J
authors.lastname: Ye
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China.|Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People's Republic of China.
authors.forename: Lan
authors.initials: L
authors.lastname: Hu
authors.affiliation: Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, People's Republic of China. licaixia@tsinghua.org.cn.|Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, 100038, Beijing, People's Republic of China. licaixia@tsinghua.org.cn.
authors.forename: Cai-Xia
authors.initials: CX
authors.lastname: Li
mesh_terms: D016172:DNA Fingerprinting / Q000379:methods*; D005787:Gene Frequency; D005828:Genetics, Population; D060148:HapMap Project; D006801:Humans; D018895:Microsatellite Repeats; D060885:Multiplex Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D044469:Racial Groups / Q000235:genetics*
keywords: Ancestry inference; Ancestry-informative markers; Multiplex assay; Population structure
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