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Cai M, Lei F, Chen M, Lan Q, Wu X, Mao C, Shi M, Zhu B. Systematic analyses of AISNPs screening and classification algorithms based on genome-wide data for forensic biogeographic ancestry inference. Forensic Sci Int 2024; 357:111975. [PMID: 38547686 DOI: 10.1016/j.forsciint.2024.111975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/23/2024] [Accepted: 03/01/2024] [Indexed: 04/06/2024]
Abstract
Identifying the biogeographic ancestral origin of biological sample left at a crime scene can provide important evidence for judicial case, as well as clue for narrowing down suspect. Ancestry informative single nucleotide polymorphism (AISNP) has become one of the most important genetic markers in recent years for screening ancestry information loci and analyzing the population genetic background and structure due to their high number and wide distributions in the human genome. In this study, based on data from 26 populations in the 1000 Genomes Project Phase 3, a Random Forest classification model was constructed with one-vs-rest classification strategy for embedded feature selection in order to obtain a panel with a small number of efficient AISNPs. The research aim was to clarify differentiations of population genetic structures among continents and subregions of East Asia. ADMIXTURE results showed that based on the 58 AISNPs selected by the machine learning algorithm, the 26 populations involved in the study could be categorized into six intercontinental ancestry components: North East Asia, South East Asia, Africa, Europe, South Asia, and America. The 24 continental-specific AISNPs and 34 East Asian-specific AISNPs were finally obtained, and used to construct the ancestry prediction model using XGBoost algorithm, resulting in the Matthews correlation coefficients of 0.94 and 0.89, and accuracies of 0.94 and 0.92, respectively. The machine learning models that we constructed using population-specific AISNPs were able to accurately predict the ancestral origins of continental and intra-East Asian populations. To summarize, screening a set of high-perform AISNPs to infer biogeographical ancestral information using embedded feature selection has potential application in creating a layered inference system that accurately differentiates from intercontinental populations to local subpopulations.
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Affiliation(s)
- Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaolian Wu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen Mao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China.
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Cai M, Li S, Zhang X, Xie W, Shi J, Yuan X, Yao J, Zhu B. Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System. J Mol Evol 2023; 91:922-934. [PMID: 38006428 DOI: 10.1007/s00239-023-10143-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/07/2023] [Indexed: 11/27/2023]
Abstract
Deletion/insertion polymorphism (DIP) is one of the more promising genetic markers in the field of forensic genetics for personal identification and biogeographic ancestry inference. In this research, we used an in-house developed ancestry-informative marker-DIP system, including 56 autosomal diallelic DIPs, three Y-chromosomal DIPs, and an Amelogenin gene, to analyze the genetic polymorphism and ancestral composition of the Chinese Korean group, as well as to explore its genetic relationships with the 26 reference populations. The results showed that this novel panel exhibited high genetic polymorphism in the studied Korean group and could be effectively applied for forensic individual identification in the Korean group. In addition, the results of multiple population genetic analyses indicated that the ancestral component of the Korean group was dominated by northern East Asia. Moreover, the Korean group was more closely related to the East Asian populations, especially to the Japanese population in Tokyo. This study enriched the genetic data of the Korean ethnic group in China and provided information on the ancestry of the Korean group from the perspective of population genetics.
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Affiliation(s)
- Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Shuanglin Li
- School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Weibing Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianfeng Shi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jun Yao
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, Liaoning, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China.
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Advancement in Human Face Prediction Using DNA. Genes (Basel) 2023; 14:genes14010136. [PMID: 36672878 PMCID: PMC9858985 DOI: 10.3390/genes14010136] [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: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.
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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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Jin XY, Liu YF, Cui W, Chen C, Zhang XR, Huang J, Zhu BF. Development a multiplex panel of AISNPs, multi-allelic InDels, microhaplotypes and Y-SNP/InDel loci for multiple forensic purposes via the NGS. Electrophoresis 2021; 43:632-644. [PMID: 34859475 DOI: 10.1002/elps.202100253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/09/2022]
Abstract
Recently, next generation sequencing showed the promising application value in forensic research. In this study, we constructed a multiplex system of different molecular genetic markers based on the previous selected AISNPs, multi-allelic InDels, microhaplotypes and Y-SNP/InDel loci and evaluated forensic efficiencies of the system in Chinese Shaanxi Han, Hui and Mongolian groups via the NGS platform. Ancestry informative analyses of Shaanxi Han, Hui and Mongolian groups revealed that most Mongolian individuals could be differentiated from Shaanxi Hans and Huis based on the selected AISNPs. Multi-allelic InDels and microhaplotypes showed the multiple allele variations and possessed relatively high genetic polymorphisms in these three groups, indicating these loci could also provide higher forensic efficiencies for individual identification and paternity testing. Based on Y-SNPs, different haplogroup distributions were observed among Shaanxi Han, Hui and Mongolian groups. In conclusion, the self-developed system could be used to simultaneously carry out the individual identification, paternity analysis, mixture deconvolution, forensic ancestry information analysis and Y chromosomal haplogroup inference, which could provide more investigative clues in forensic practices. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xiao-Ye Jin
- Xi'an Jiaotong University Health Science Center, Xi'an, P. R. China.,Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yan-Fang Liu
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Wei Cui
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chong Chen
- Xi'an Jiaotong University Health Science Center, Xi'an, P. R. China
| | - Xing-Ru Zhang
- Xi'an Jiaotong University Health Science Center, Xi'an, P. R. China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Bo-Feng Zhu
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
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Chen C, Jin X, Zhang X, Zhang W, Guo Y, Tao R, Chen A, Xu Q, Li M, Yang Y, Zhu B. Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers. Front Genet 2021; 12:705753. [PMID: 34721519 PMCID: PMC8555763 DOI: 10.3389/fgene.2021.705753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy-Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Min Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Department of Forensic Genetics, Multi-Omics Innovative Research Center of Forensic Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Jin X, Liu Y, Zhang Y, Li Y, Chen C, Wang H. Autosomal deletion/insertion polymorphisms for global stratification analyses and ancestry origin inferences of different continental populations by machine learning methods. Electrophoresis 2021; 42:1473-1479. [PMID: 33948979 DOI: 10.1002/elps.202100044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 11/11/2022]
Abstract
A lot of population data of 30 deletion/insertion polymorphisms (DIPs) of the Investigator DIPplex kit in different continental populations have been reported. Here, we assessed genetic distributions of these 30 DIPs in different continental populations to pinpoint candidate ancestry informative DIPs. Besides, the effectiveness of machine learning methods for ancestry analysis was explored. Pairwise informativeness (In) values of 30 DIPs revealed that six loci displayed relatively high In values (>0.1) among different continental populations. Besides, more loci showed high population-specific divergence (PSD) values in African population. Based on the pairwise In and PSD values of 30 DIPs, 17 DIPs in the Investigator DIPplex kit were selected to ancestry analyses of African, European, and East Asian populations. Even though 30 DIPs provided better ancestry resolution of these continental populations based on the results of PCA and population genetic structure, we found that 17 DIPs could also distinguish these continental populations. More importantly, these 17 DIPs possessed more balanced cumulative PSD distributions in these populations. Six machine learning methods were used to perform ancestry analyses of these continental populations based on 17 DIPs. Obtained results revealed that naïve Bayes manifested the greatest performance; whereas, k nearest neighbor showed relatively low performance. To sum up, these machine learning methods, especially for naïve Bayes, could be used as the valuable tool for ancestry analysis.
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Affiliation(s)
- Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China.,Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital,Zhengzhou University People's Hospital, Zhengzhou, P. R. China.,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, P. R. China
| | - Yuluo Liu
- Department of Forensic Science, Guangdong Police College, Guangzhou, P. R. China
| | - Yuanyuan Zhang
- School of Foreign Languages, Zhengzhou University of Industrial Technology, Zhengzhou, P. R. China
| | - Yongle Li
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, P. R. China
| | - Chuanliang Chen
- Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, P. R. China
| | - Hongdan Wang
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital,Zhengzhou University People's Hospital, Zhengzhou, P. R. China.,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, P. R. China
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8
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Special Issue "Forensic Genetics and Genomics". Genes (Basel) 2021; 12:genes12020158. [PMID: 33503983 PMCID: PMC7912074 DOI: 10.3390/genes12020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 01/23/2021] [Indexed: 11/16/2022] Open
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Jin X, Zhang X, Shen C, Liu Y, Cui W, Chen C, Guo Y, Zhu B. A Highly Polymorphic Panel Consisting of Microhaplotypes and Compound Markers with the NGS and Its Forensic Efficiency Evaluations in Chinese Two Groups. Genes (Basel) 2020; 11:genes11091027. [PMID: 32883034 PMCID: PMC7565596 DOI: 10.3390/genes11091027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Novel genetic markers like microhaplotypes and compound markers show promising potential in forensic research. Based on previously reported single nucleotide polymorphism (SNP) and insertion/deletion (InDel) polymorphism loci, 29 genetic markers including 22 microhaplotypes and seven compound markers were identified. Genetic distributions of the 29 loci in five continental populations, Kazak and Mongolian groups in China were investigated. We found that the expected heterozygosity values of these 29 loci were >0.4 in these populations, indicating these loci were relatively high polymorphisms. Population genetic analyses of five continental populations showed that five loci displayed relatively high genetic variations among these continental populations and could be useful markers for ancestry analysis. In summary, the 29 loci displayed relatively high genetic diversities in continental populations and Chinese two groups and could be informative loci for forensic research.
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Affiliation(s)
- Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Chunmei Shen
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi’an 710062, China;
| | - Yanfang Liu
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- Correspondence: ; Tel.: +86-020-61648787
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