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Hao WQ, Liu J, Jiang L, Han JP, Wang L, Li JL, Ma Q, Liu C, Wang HJ, Li CX. Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs. Int J Legal Med 2018; 133:975-982. [PMID: 29882060 DOI: 10.1007/s00414-018-1863-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 05/14/2018] [Indexed: 01/05/2023]
Abstract
Inferring an unknown DNA's ancestry using a set of ancestry-informative single nucleotide polymorphisms (SNPs) in forensic science is useful to provide investigative leads. This is especially true when there is no DNA database match or specified suspect. Thus, a set of SNPs with highly robust and balanced differential power is strongly demanded in forensic science. In addition, it is also necessary to build a genotyping database for estimating the ancestry of an individual or an unknown DNA. For the differentiation of Africans, Europeans, East Asians, Native Americans, and Oceanians, the Global Nano set that includes just 31 SNPs was developed by de la Puente et al. Its ability for differentiation and balance was evaluated using the genotype data of the 1000 Genomes Phase III project and the Stanford University HGDP-CEPH. Just 402 samples were genotyped and analyzed as a reference set based on statistical methods. To validate the differentiating capacity using more samples, we developed a single-tube 28-plex SNP assay in which the SNPs were chosen from the 31 allelic loci of the Global AIMs Nano set. Three tri-allelic SNPs used to differentiate mixed-source DNA contribute little to population differentiation and were excluded here. Then, 998 individuals from 21 populations were typed, and these genotypes were combined with the genotype data obtained from 1000 Genomes Phase III and the Stanford University HGDP-CEPH (3090 total samples,43 populations) to estimate the power of this multiplex assay and build a database for the further inference of an individual or an unknown DNA sample in forensic practice.
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Affiliation(s)
- Wei-Qi Hao
- Institute of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Jing Liu
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Li Jiang
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Jun-Ping Han
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
- Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau, Beijing, 100102, China
| | - Ling Wang
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Jiu-Ling Li
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Quan Ma
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Chao Liu
- Institute of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, Guangdong, China.
| | - Hui-Jun Wang
- Institute of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Cai-Xia Li
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China.
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Peng MS, Xu W, Song JJ, Chen X, Sulaiman X, Cai L, Liu HQ, Wu SF, Gao Y, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Wu M, Li GM, Yang XY, Rakha A, Yao YG, Upur H, Zhang YP. Mitochondrial genomes uncover the maternal history of the Pamir populations. Eur J Hum Genet 2017; 26:124-136. [PMID: 29187735 DOI: 10.1038/s41431-017-0028-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 09/08/2017] [Accepted: 10/06/2017] [Indexed: 12/22/2022] Open
Abstract
The Pamirs, among the world's highest mountains in Central Asia, are one of homelands with the most extreme high altitude for several ethnic groups. The settlement history of modern humans on the Pamirs remains still opaque. Herein, we have sequenced the mitochondrial DNA (mtDNA) genomes of 382 individuals belonging to eight populations from the Pamirs and the surrounding lowlands in Central Asia. We construct the Central Asian (including both highlanders and lowlanders) mtDNA haplogroup tree at the highest resolution. All the matrilineal components are assigned into the defined mtDNA haplogroups in East and West Eurasians. No basal lineages that directly emanate from the Eurasian founder macrohaplogroups M, N, and R are found. Our data support the origin of Central Asian being the result of East-West Eurasian admixture. The coalescence ages for more than 93% mtDNA lineages in Central Asians are dated after the last glacial maximum (LGM). The post-LGM and/or later dispersals/admixtures play dominant roles in shaping the maternal gene pool of Central Asians. More importantly, our analyses reveal the mtDNA heterogeneity in the Pamir highlanders, not only between the Turkic Kyrgyz and the Indo-European Tajik groups, but also among three highland Tajiks. No evidence supports positive selection or relaxation of selective constraints in the mtDNAs of highlanders as compared to that of lowlanders. Our results suggest a complex history for the peopling of Pamirs by multiple waves of migrations from various genetic resources during different time scales.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Weifang Xu
- Key Laboratory of the Chinese Ministry of Education and Xinjiang Uighur Autonomous Region for High-Incident Diseases in Uighur Ethnic Population, Xinjiang Medical University, Urumqi, 830011, China.,Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, 830000, China
| | - Jiao-Jiao Song
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Xing Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | - Liuhong Cai
- The Second People's Hospital of Kashi, Kashi, 844000, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Najmudinov Tojiddin Abdulloevich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Khudoidodov Behruz Ibrohimovich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Miao Wu
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xing-Yan Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Allah Rakha
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China.,Department of Forensic Sciences, University of Health Sciences, Lahore, 54600, Pakistan
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Halmurat Upur
- Key Laboratory of the Chinese Ministry of Education and Xinjiang Uighur Autonomous Region for High-Incident Diseases in Uighur Ethnic Population, Xinjiang Medical University, Urumqi, 830011, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
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