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Zhang H, Yang M, Zhang H, Ren Z, Wang Q, Liu Y, Jin X, Ji J, Feng Y, Cai C, Ran Q, Li C, Huang J. Forensic features and phylogenetic structure survey of four populations from southwest China via the autosomal insertion/deletion markers. Forensic Sci Res 2024; 9:owad052. [PMID: 38765700 PMCID: PMC11102079 DOI: 10.1093/fsr/owad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/09/2023] [Indexed: 05/22/2024] Open
Abstract
Insertion/Deletion (InDel) polymorphisms, characterized by their smaller amplicons, reduced mutation rates, and compatibility with the prevalent capillary electrophoresis (CE) platforms in forensic laboratories, significantly contribute to the advancement and application of genetic analysis. Guizhou province in China serves as an important region for investigating the genetic structure, ethnic group origins, and human evolution. However, DNA data and the sampling of present-day populations are lacking, especially about the InDel markers. Here, we reported data on 47 autosomal InDels from 592 individuals from four populations in Guizhou (Han, Dong, Yi, and Chuanqing). Genotyping was performed with the AGCU InDel 50 kit to evaluate their utility for forensic purposes and to explore the population genetic structure. Our findings showed no significant deviations from Hardy-Weinberg and linkage equilibriums. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) for each population demonstrated that the kit could be applied to forensic individual identification and was an effective supplement for parentage testing. Genetic structure analyses, including principal component analysis, multidimensional scaling, genetic distance calculation, STRUCTURE, and phylogenetic analysis, highlighted that the genetic proximity of the studied populations correlates with linguistic, geographical, and cultural factors. The observed genetic variances within four research populations were less pronounced than those discerned between populations across different regions. Notably, the Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi. These results underscore the potential of InDel markers in forensic science and provide insights into the genetic landscape and human evolution in multi-ethnic regions like Guizhou. Key points InDel markers show promise for forensic individual identification and parentage testing via the AGCU InDel 50 kit.Genetic analysis of Guizhou populations reveals correlations with linguistic, geographical, and cultural factors.Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi.
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Affiliation(s)
- Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Changsheng Cai
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qianchong Ran
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Jiang Huang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
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Wu H, Wang K, Zhang L, Fan A. Genetic and structural characterization of 20 autosomal STR loci from the Henan Han population of central China. Ann Hum Biol 2022; 49:80-86. [PMID: 35038931 DOI: 10.1080/03014460.2022.2030406] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
AIM This study was designed to investigate the genetic polymorphisms and forensic parameters of the 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 System (Promega, USA) in the Henan Han population with a view to expand the genetic information available for this population in human genome databases. SUBJECTS AND METHODS We evaluated the genetic polymorphisms from 20 autosomal STR loci using DNA typing based on 2995 individuals from the Henan Han population in central China and then used this information to investigate the genetic relationships between this population and the other 10 Han populations across China. These comparisons included genetic distance, phylogenetic trees, and principal component analysis (PCA). RESULTS We identified a total of 290 alleles and 1343 genotypes within the Henan Han population, with none of these loci deviating from their Hardy-Weinberg equilibrium (HWE). The population comparisons revealed that geographically close populations demonstrated closer genetic relationships. Thus, the Henan Han population was shown to be close to both the Beijing Han and Tianjin Han populations, creating a single cluster. In addition, these 20 STR loci exhibited a high degree of genetic polymorphisms, making them suitable for individual identification and parentage testing. CONCLUSIONS The results of this study will enrich the forensic databases of Chinese Han populations and serve as a resource for further studies in these populations.
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Affiliation(s)
- Hongyan Wu
- School of Forensic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China.,Xinxiang Key Laboratory of Forensic Science Evidence, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Kejie Wang
- School of Forensic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Lin Zhang
- School of Forensic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China.,Xinxiang Key Laboratory of Forensic Science Evidence, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Aiying Fan
- School of Forensic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
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Long J. Parentage analysis using genome-wide high-density SNP microarray. Gene 2021; 785:145605. [PMID: 33771603 DOI: 10.1016/j.gene.2021.145605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/01/2021] [Accepted: 03/17/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Parentage analysis is a technology that uses genetic methods to verify or exclude relationships between individuals. STR technology is often used in parentage analysis. We received three sets of samples from three families. Each set of samples consisted of a male individual and a female individual. Their test requirements were meant to determine whether they were a paternity relationship, a sibling relationship, or grandparent-grandchild relationship. However, only one STR locus mismatch was detected in each group. Other family members to assist in testing could not be identified; therefore, other methods were needed to assist in judgment. Using high-density SNP microarrays, we analyzed the feasibility of its application in paternity analysis. RESULTS A total of 180 samples were tested, including 100 unrelated samples, and 74 samples from 30 families, and six samples from three families. The data were analyzed, grouped according to the chromosome of SNP, and the mismatching rate was counted. The total mismatching rate of SNP in unrelated individuals was 8-10 times higher than that of parent-child individuals. Individuals with a total mismatch rate of more than 5.3% were defined as individuals with no kinship, and the individuals with a total mismatch rate of less than 0.6% were defined as the individuals with a parent-child relationship. CONCLUSIONS Through the use of high-density gene chips for analysis, we also completed an auxiliary analysis of the kinship of the three families. The gene chip is a better method for auxiliary analysis of the kinship between individuals.
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Affiliation(s)
- Ju Long
- Xi'an Jiaotong University School of Basic Medical Sciences, Xi'an, Shaanxi 710061, PR China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China; Laboratory of Forensic, Judicial Authentication Institute of Qinzhou Jin Hai Wan, Qinzhou, Guangxi 535099, PR China; Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi 535099, PR China.
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Wu R, Li H, Li R, Peng D, Wang N, Shen X, Sun H. Identification and sequencing of 59 highly polymorphic microhaplotypes for analysis of DNA mixtures. Int J Legal Med 2021; 135:1137-1149. [PMID: 33502549 DOI: 10.1007/s00414-020-02483-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/09/2020] [Indexed: 12/30/2022]
Abstract
Mixture detection remains one of the major challenges within a forensic science context. In recent years, microhaplotypes were proposed to have great potential in mixture detection, although many of them are not as polymorphic as widely used short tandem repeat (STR) markers. In this study, 59 new highly polymorphic microhaplotypes were identified and sequenced with the NextSeq 500 Sequencer. Based on the whole 1000 Genomes Project dataset, the average effective number of alleles (Ae) of the 59 microhaplotypes was 5.44, and the Ae values of 36 of these microhaplotypes were > 5.00. Their genetic variations in 187 Han Chinese individuals were evaluated. The average allele coverage ratio (ACR) of heterozygotes across all loci was 0.96 ± 0.05. The number of observed alleles varied from 4 to 23, with an average of 8.8 alleles per microhaplotype locus. The average observed heterozygosity (Ho) of 59 loci was 0.77 ± 0.05, and the Ho values of 15 of these loci were > 0.80. All loci showed high polymorphisms with a discrimination power (DP) ranging from 0.80 to 0.97, and the average DP was 0.92 ± 0.03. The analysis of simulated mixtures demonstrated that the microhaplotypes reported here were highly polymorphic and performed well in forensic DNA mixture analysis. This study not only demonstrated the applicability of microhaplotypes in mixture analysis but also provided new choices for highly polymorphic microhaplotypes because after adding the markers identified here, the number of microhaplotypes with Ae values of > 4.00 will increase from ~ 50 to ~ 110.
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Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.
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Pan M, Ye Q, Ju XB, Cui H, Zhou HY. Population genetic polymorphism and mutation analysis of 19 autosomal STR loci in Jiangsu Han individuals in Eastern China. Ann Hum Biol 2019; 46:272-278. [PMID: 31208213 DOI: 10.1080/03014460.2019.1632929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Aim: Genetic polymorphisms and the mutation ratio of 19 autosomal short tandem repeat (STR) loci were analysed in 10,000 individuals and 7755 families from Jiangsu Province in Eastern China.Subjects and methods: Nineteen STR loci were amplified by a multiplex amplification system and genotyped on the ABI 3130 Genetic Analyser. Allele frequencies, forensic parameters and mutations for the 19 autosomal STR loci were statistically analysed.Results: In total, 344 genotypes were discovered. No significant deviation from Hardy-Weinberg equilibrium was observed. The combined power of discrimination reached 0.9999999999999999984341, and the combined probability of paternity exclusion was 0.999999989. The pairwise genetic distance and p-values between the Jiangsu and 17 published populations depended on the FST value calculation and are shown by the neighbour-joining evolutionary tree. No statistically significant differences were found, except for the Xinjiang Altay Han (p = 0.01802) population. The average mutation rate of the Jiangsu population across all 19 loci was 1.4 × 10-3. The average mutation rate of the 13 core CODIS STR loci remained below 2 × 10-3 and there was no difference and relatively high consistency (p < 0.001) by correlation coefficient analysis among the six groups.Conclusions: Allelic genetic polymorphisms and mutation data were obtained from a large number of samples, which indicated that the amplification kit is suitable for forensic application and that the Jiangsu population has its own genetic characteristics that are different from those of other ethnic populations.
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Affiliation(s)
- Meng Pan
- Jiangsu Province Hospital Judicial Identification, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China.,Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Qin Ye
- Jiangsu Province Hospital Judicial Identification, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Xiao-Bin Ju
- Jiangsu Province Hospital Judicial Identification, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - He Cui
- Jiangsu Province Hospital Judicial Identification, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Hui-Ying Zhou
- Jiangsu Province Hospital Judicial Identification, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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