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Wang J, Yang L, Duan S, Sun Q, Li Y, Wu J, Wu W, Wang Z, Liu Y, Tang R, Yang J, Liu C, Yuan B, Wang D, Xu J, Wang M, He G. Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China. Hum Genomics 2023; 17:3. [PMID: 36721228 PMCID: PMC9887792 DOI: 10.1186/s40246-023-00452-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/22/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized. OBJECTIVES To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling. RESULTS The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways. CONCLUSIONS Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.
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Affiliation(s)
- Jiawen Wang
- grid.413458.f0000 0000 9330 9891College of Forensic Medicine, Guizhou Medical University, Guiyang, 550004 China
| | - Lin Yang
- grid.413458.f0000 0000 9330 9891College of Forensic Medicine, Guizhou Medical University, Guiyang, 550004 China
| | - Shuhan Duan
- grid.449525.b0000 0004 1798 4472School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000 China
| | - Qiuxia Sun
- grid.203458.80000 0000 8653 0555Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331 China
| | - Youjing Li
- grid.411634.50000 0004 0632 4559Congjiang People’s Hospital, Congjiang, 557499 China
| | - Jun Wu
- grid.413458.f0000 0000 9330 9891College of Forensic Medicine, Guizhou Medical University, Guiyang, 550004 China
| | - Wenxin Wu
- grid.413458.f0000 0000 9330 9891College of Forensic Medicine, Guizhou Medical University, Guiyang, 550004 China
| | - Zheng Wang
- grid.13291.380000 0001 0807 1581Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610000 China
| | - Yan Liu
- grid.13291.380000 0001 0807 1581Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041 China ,grid.449525.b0000 0004 1798 4472School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000 China
| | - Renkuan Tang
- grid.203458.80000 0000 8653 0555Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331 China
| | - Junbao Yang
- grid.449525.b0000 0004 1798 4472School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000 China
| | - Chao Liu
- grid.12981.330000 0001 2360 039XFaculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Buhong Yuan
- Longli People’s Hospital, Longli, 551299 China
| | - Daoyong Wang
- Nayong Guohua Yixin Hospital, Nayong, 553306 China
| | - Jianwei Xu
- Department of Pharmacology, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China.
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
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Chen M, Lan Q, Nie S, Hu L, Fang Y, Cui W, Bai X, Liu L, Zhu B. Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel. Front Genet 2023; 13:1057231. [PMID: 36685924 PMCID: PMC9845582 DOI: 10.3389/fgene.2022.1057231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 01/06/2023] Open
Abstract
Deletion/insertion polymorphism (DIP), as a short insertion/deletion sequence polymorphic genetic marker, has attracted the attention of forensic genetic scientist due to its lack of stutter, short amplicon and abundant ancestral information. In this study, based on a self-developed 43 autosomal deletion/insertion polymorphism (A-DIP) loci panel which could meet the forensic application purposes of individual identification, kinship testing and ancestral inference to some extent, we evaluated the forensic efficiencies of the above three forensic objectives in Chinese Yi, Hani and Miao groups of Yunnan province. The cumulative match probability (CPM) and combined probability of exclusion (CPE) of these three groups were 1.11433E-18, 8.24299E-19, 4.21721E-18; 0.999610217, 0.999629285 and 0.999582084, respectively. Average 96.65% full sibling pairs could be identified from unrelated individual pairs (as likelihood ratios > 1) using this DIP panel, whereas the average false positive rate was 3.69% in three target Yunnan groups. With the biogeographical ancestor prediction models constructed by extreme gradient boosting (XGBoost) and support vector machine (SVM) algorithms, 0.8239 (95% CI 0.7984, 0.8474) of the unrelated individuals could be correctly divided according to the continental origins based on the 43 A-DIPs which were large frequency distribution differentiations among different continental populations. The present results of principal component analysis (PCA), multidimensional scaling (MDS), neighbor joining (NJ) and maximum likelihood (ML) phylogenetic trees and STRUCTURE analyses indicated that these three Yunnan groups had relatively close genetic distances with East Asian populations.
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Affiliation(s)
- Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qiong Lan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Yating Fang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaole Bai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Liu Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China,*Correspondence: Bofeng Zhu,
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Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.
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Forensic efficacy evaluation and genetic structure exploration of the Yunnan Miao group by a multiplex InDel panel. Electrophoresis 2022; 43:1765-1773. [DOI: 10.1002/elps.202100387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/08/2022] [Accepted: 05/19/2022] [Indexed: 11/07/2022]
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Liu J, Zhang X, Zhang X, Li W, Gao L, Li J, Wang J, Liu Z, Liu Y, Yan J, Zhang G. A new set of 20 Multi‐InDel markers for forensic application. Electrophoresis 2022; 43:1193-1202. [DOI: 10.1002/elps.202100361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Jinding Liu
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Xiuying Zhang
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Xiaomeng Zhang
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Wenyan Li
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Linlin Gao
- Institute of Criminal Science and Technology of Hangzhou Public Security Bureau Hangzhou P. R. China
| | - Jing Li
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Jiaqi Wang
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Zidong Liu
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Yao Liu
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
| | - Gengqian Zhang
- School of Forensic Medicine Shanxi Medical University Jinzhong Shanxi P. R. China
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Lan Q, Zhao C, Chen C, Xu H, Fang Y, Yao H, Zhu B. Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set. Front Genet 2022; 13:816737. [PMID: 35601485 PMCID: PMC9121381 DOI: 10.3389/fgene.2022.816737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
The MPS technology has expanded the potential applications of DNA markers and increased the discrimination power of the targeted loci by taking variations in their flanking regions into consideration. Here, a collection of nuclear and extranuclear DNA markers (totally six kinds of nuclear genetic markers and mtDNA hypervariable region variations) were comprehensively and systematically assessed for polymorphism detections, further employed to dissect the population backgrounds in the Yugu ethnic group from Gansu province (Yugu) and Han population from the Inner Mongolia Autonomous Region (NMH) of China. The elevated efficiencies of the marker set in separating full sibling and challenging half sibling determination cases in parentage tests (iiSNPs), as well as predicting ancestry origins of unknown individuals from at least four continental populations (aiSNPs) and providing informative characteristic-related clues for Chinese populations (piSNPs) are highlighted in the present study. To sum up, different sets of DNA markers revealed sufficient effciencies to serve as promising tools in forensic applications. Genetic insights from the perspectives of autosomal DNA, Y chromosomal DNA, and mtDNA variations yielded that the Yugu ethnic group was genetically close related to the Han populations of the northern region. But we admit that more reference populations (like Mongolian, Tibetan, Hui, and Tu) should be incorporated to gain a refined genetic background landscape of the Yugu group in future studies.
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Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Congying Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chong Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yating Fang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Bofeng Zhu,
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Cai Y, Zhang S, Zhang J, Liu X, Ma K, Xu W, Deng X, Yang J, Ma T, Jiang C, Hui W, Cui Y. Visual Detection of ACE I/D Polymorphism Using T-ARMS-PCR Combined with a Lateral Flow Assay and Its Clinical Application. Anal Chem 2022; 94:4686-4694. [PMID: 35271257 DOI: 10.1021/acs.analchem.1c04817] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Insertions/deletions (indels) variations have been recognized as a promising marker for the development of various diseases. However, methods used for the genotyping of indels in studies were tedious, complicated, and required sophisticated or expensive instruments, as well as complex data analysis, which makes it difficult to meet the demand of point of care testing. Herein, we presented a fast and accurate biosensor (T-ARMS-PCR-LFA) by the combination of tetra-primer amplification refractory mutation system polymerase chain reaction (T-ARMS-PCR) and GoldMag lateral flow assay (LFA) for visual genotyping of ACE I/D polymorphism. ACE I/D can be distinguished by employing four primers in one PCR reaction, and genotyping results were presented by the visual inspection of colors on the nitrocellulose membrane of LFA strips within 5 min. And 50 of the human genomic DNA samples were used for the detection of ACE I/D to further validate the accuracy of the T-ARMS-PCR-LFA system. As a demonstration, we showed that ACE I/D could be genotyped using a low amount of DNA sample (25 ng) with an accuracy of 100%, without complicated operation steps and data analysis, which is better than that of the conventional method (agarose gel electrophoresis analysis after common PCR). In conclusion, the biosensor is highly applicable for genotyping specific large indel variants in clinical practices, which enables rapid clinical decision-making, improves the management of disease diagnosis, and facilitates personalized medicine.
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Affiliation(s)
- Yu Cai
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,National Engineering Research Center for Miniaturized Detection System, Xi'an, Shaanxi 710069, China
| | - Sinong Zhang
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,National Engineering Research Center for Miniaturized Detection System, Xi'an, Shaanxi 710069, China
| | - Jiaxing Zhang
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,National Engineering Research Center for Miniaturized Detection System, Xi'an, Shaanxi 710069, China
| | - Xiaonan Liu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,National Engineering Research Center for Miniaturized Detection System, Xi'an, Shaanxi 710069, China
| | - Kang Ma
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,National Engineering Research Center for Miniaturized Detection System, Xi'an, Shaanxi 710069, China
| | - Wei Xu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,National Engineering Research Center for Miniaturized Detection System, Xi'an, Shaanxi 710069, China
| | - Xianghai Deng
- Department of Clinical Laboratory, Ankang Hospital of Traditional Chinese Medicine, Ankang, Shaanxi 725099, China
| | - Jiangcun Yang
- Department of Blood Transfusion, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, China
| | - Ting Ma
- Department of Blood Transfusion, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, China
| | - Chao Jiang
- The Second Affiliated Hospital of Xi'an Medical University and Shaanxi Key Laboratory of Brain Disorders, Xi'an, Shaanxi 710038, China
| | - Wenli Hui
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,National Engineering Research Center for Miniaturized Detection System, Xi'an, Shaanxi 710069, China
| | - Yali Cui
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,National Engineering Research Center for Miniaturized Detection System, Xi'an, Shaanxi 710069, China
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Liu Y, Jin X, Lan Q, Zhao C, Xu H, Xie T, Lan J, Tai Y, Zhu B. Forensic characteristic and population structure dissection of Shaanxi Han population in the light of diallelic deletion/insertion polymorphism data. Genomics 2020; 112:3837-3845. [PMID: 32574833 DOI: 10.1016/j.ygeno.2020.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/08/2022]
Abstract
The genetic polymorphisms of diallelic deletion/insertion polymorphic (DIP) loci in the Shaanxi Han population are still not clearly characterized. Herein, allele frequencies and forensic application efficiencies for 30 diallelic DIP loci were investigated in 506 unrelated healthy Han individuals from Chinese Shaanxi province. Based on population data of the same 30 diallelic DIP loci, the genetic differentiations, hierarchical clustering relationships and population architectures among Shaanxi Han and other 50 populations were further dissected through genetic and bioinformatics analyses. Results indicated that most of the 30 diallelic DIP loci were relatively high polymorphisms in the Shaanxi Han population; and there were the genetically intimate relationships between Shaanxi Han and the East Asian populations. In summary, this study provided significant insights into genetic background of Shaanxi Han population, and the multiplex amplification of these 30 diallelic DIP loci was appropriate for forensic individual identification and population genetic research in Shaanxi Han population.
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Affiliation(s)
- Yanfang Liu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004 Xi'an, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Qiong Lan
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Congying Zhao
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Hui Xu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Tong Xie
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jiangwei Lan
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yunchun Tai
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004 Xi'an, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.
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