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Tan M, Xue J, Wu Q, Zheng Y, Liu G, Zhang R, Wu M, Song J, Xiao Y, Chen D, Lv M, Liao M, Qu S, Liang W. Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing. Electrophoresis 2024; 45:463-473. [PMID: 37946554 DOI: 10.1002/elps.202300195] [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: 09/04/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300 bp. Further, we successfully developed and evaluated an NGS-based panel comprising 55 loci, of which 24 were composed of both SNPs and InDels. Analysis of 124 unrelated Southern Han Chinese revealed an average effective number of alleles (Ae ) of 7.52 for this panel. The cumulative power of discrimination and cumulative probability of exclusion values of the 55 loci were 1-2.37 × 10-73 and 1-1.19 × 10-28 , respectively. Additionally, this panel exhibited high allele detection rates of over 97% in each of the 21 artificial mixtures involving from two to six contributors at different mixing ratios. We used EuroForMix to calculate the likelihood ratio (LR) and evaluate the evidence strength provided by this panel, and it could assess evidence strength with LR, distinguishing real and noncontributors. In conclusion, our panel holds great potential for detecting and analyzing DNA mixtures in forensic applications, with the capability to enhance routine mixture analysis.
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Affiliation(s)
- Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Mengna Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jinlong Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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Population Genetic Data of 30 Insertion-Deletion Markers in the Polish Population. Genes (Basel) 2022; 13:genes13101683. [PMID: 36292568 PMCID: PMC9601377 DOI: 10.3390/genes13101683] [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: 08/30/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included in the Investigator DIPplex kit (Qiagen) were obtained in a sample of 631 unrelated Polish individuals. Allelic frequency data were compared with those reported for selected populations (3) Results: All the loci conformed with Hardy-Weinberg equilibrium after applying a Bonferroni correction and no pair-wise significant linkage disequilibrium was detected. (4) Conclusions: DIPplex Kit differences were high among populations worldwide. The InDel markers are highly discriminating for human identification purposes in the Polish population.
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Yang M, Yang X, Ren Z, He G, Zhang H, Wang Q, Liu Y, Zhang H, Ji J, Chen J, Guo J, Huang J, Wang CC. Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.
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Zhao C, Yang J, Xu H, Mei S, Fang Y, Lan Q, Deng Y, Zhu B. Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel. J Zhejiang Univ Sci B 2022; 23:241-248. [PMID: 35261219 DOI: 10.1631/jzus.b2100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Due to the virtues of no stutter peaks, low rates of mutation, and short amplicon sizes, insertion/deletion (InDel) polymorphism is an indispensable tool for analyzing degraded DNA samples from crime scenes for human identifications (Wang et al., 2021). Herein, a self-developed panel of 43 InDel loci constructed previously by our group was utilized to evaluate the genetic diversities and explore the genetic background of the Han Chinese from Beijing (HCB) including 301 random healthy individuals. The lengths of amplicons at 43 InDel loci in this panel ranged from 87 to 199 bp, which indicated that the panel could be used as an effective tool to utilize highly degraded DNA samples for human identity testing. The loci in this panel were validated and performed well for forensic degraded DNA samples (Jin et al., 2021). The combined discrimination power (PD) and combined probability of exclusion (PE) values in this panel indicated that the 43 InDel loci could be used as the candidate markers in personal identification and parentage testing of HCB. In addition, population genetic relationships between the HCB and 26 reference populations from five continents based on 19 overlapped InDel loci were displayed by constructing a phylogenetic tree, principal component analysis (PCA), and population genetic structure analysis. The results illustrated that the HCB had closer genetic relationships with the Han populations from Chinese different regions.
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Affiliation(s)
- Congying Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jinlong Yang
- Beijing Zhongzheng DNA Evidence Institute, Beijing 101318, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Shuyan Mei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yating Fang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yajun Deng
- Beijing Zhongzheng DNA Evidence Institute, Beijing 101318, China. ,
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, 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, Xi'an 710004, 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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Cui W, Jin X, Guo Y, Chen C, Zhang W, Kong T, Wang Y, Huang J, Zhu B. Forensic applicability of autosomal insertion/deletion loci in Chinese Daur ethnic group and genetic affinity evaluations between Daur group and reference populations. Leg Med (Tokyo) 2020; 47:101741. [PMID: 32682294 DOI: 10.1016/j.legalmed.2020.101741] [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: 06/27/2019] [Revised: 04/01/2020] [Accepted: 06/26/2020] [Indexed: 12/25/2022]
Abstract
In present study, we evaluated the genetic diversities of 30 insertion/deletion (InDel) loci and analyzed the genetic relationships between Daur and other comparison populations. In the studied Daur group, any two InDel loci showed no linkage disequilibrium, and all loci showed no deviations from exact tests of Hardy-Weinberg equilibrium. Insertion allele frequencies at 30 InDel loci ranged from 0.1459 (HLD39) to 0.8774 (HLD118). The observed heterozygosity and expected heterozygosity values were ranged from 0.1984 (HLD118) to 0.5564 (HLD6) and 0.2155 (HLD118) to 0.5000 (HLD92 and HLD6), respectively. The combined power of discrimination and power of exclusion values were 0.999999999993428 and 0.9878, respectively, which indicated that this panel of 30 InDels could be used for individual identifications in Daur group. Population genetic analyses including pairwise fixation index, STRUCTURE analysis, principal component analysis, genetic distance, multidimensional scaling analysis and phylogenetic analysis demonstrated that the Daur group had the closer genetic relationships with the groups from western China in comparison with other continental populations.
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Affiliation(s)
- Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Tingting Kong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Yijie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Jingfeng Huang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
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Taha T, Elzalabany S, Fawzi S, Hisham A, Amer K, Shaker O. Allele frequency comparative study between the two main Egyptian ethnic groups. Forensic Sci Int 2020; 313:110348. [PMID: 32521421 DOI: 10.1016/j.forsciint.2020.110348] [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: 04/29/2020] [Accepted: 05/24/2020] [Indexed: 11/17/2022]
Abstract
The study of genetic correlation between ethnic groups, constituting one nation, is an important issue. This work aims to study the correlation between allele frequencies of nine Short Tandem Repeats (STRs) autosomal loci (D3S1358, VWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, and D7S820) for the main two Egyptian ethnic groups, Muslims and Christians, in order to test the hypothesis of a common ancestral for the whole Egyptian population. Each group is represented by a sample of 100 unrelated healthy individuals. The genetic correlation of the two ethnic groups is investigated using alleles' frequencies statistics, forensic efficiency parameters and populations' homogeneity charts. Graphical methods were used to check the harmony between the two ethnic groups. The results support that Egyptian Muslims and Egyptian Christians genetically originate from the same ancestors.
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Affiliation(s)
- Tarek Taha
- Department of Immune Diseases, Egyptian Army Central Medical Laboratories, Cairo, Egypt
| | - Sagy Elzalabany
- Egypt Center for Research and Regenerative Medicine, Cairo, Egypt
| | - Sahar Fawzi
- Department of Systems and Biomedical Engineering, Faculty of Engineering, CairoUniversity, Cairo 12613, Egypt
| | - Ahmed Hisham
- Department of Systems and Biomedical Engineering, Faculty of Engineering, CairoUniversity, Cairo 12613, Egypt
| | - Khaled Amer
- Egypt Center for Research and Regenerative Medicine, Cairo, Egypt
| | - Olfat Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt.
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Liu J, Hao T, Cheng X, Wang J, Li W, Liu Z, Shi J, Li Z, Ren J, Yun K, Zhang G. DIP-microhaplotypes: new markers for detection of unbalanced DNA mixtures. Int J Legal Med 2020; 135:13-21. [PMID: 32372232 DOI: 10.1007/s00414-020-02288-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022]
Abstract
The identification of a suspect in a degraded and unbalanced DNA mixture has been a challenge for the standard short tandem repeat polymorphisms (STR) typing. Several methods have been introduced to solve this problem, such as DIP-STR, DIP-SNP, and SNP-STR markers. In this study, we proposed DIP-microhaplotype (deletion/insertion linked a chain of SNPs) as a kind of new genetic marker to type the unbalanced and degraded DNA mixture. We established the detection method with ten DIP-microhaplotype markers including 26 SNPs using allele-specific multiplex PCR followed by SNaPshot assay. This novel compound marker allows us to detect the minor DNA with a sensitivity of 1:100 to 1:1000 in a DNA mixture of any gender. Most of the DIP-microhaplotype markers had a relatively high probability of informative alleles with an average informative value (I value) of 0.308. In all, we proposed DIP-microhaplotype as a novel type of DNA marker for the detection of minor contributor from unbalanced DNA mixtures. Due to their inherent shorter length, higher polymorphism, and sensitivity, DIP-microhaplotypes are promising markers for the examination of the degraded and unbalanced mixtures in forensic stains or clinical chimeras.
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Affiliation(s)
- Jinding Liu
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Ting Hao
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Xiaojuan Cheng
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Jiaqi Wang
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Wenyan Li
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Zidong Liu
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Jie Shi
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Zeqin Li
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Jianbo Ren
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Keming Yun
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China.
| | - Gengqian Zhang
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China.
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Wang F, He G, Wang Z, Wang M, Liu J, Zou X, Wang S, Song M, Ye Z, Xie M, Hou Y. Population genetics and forensic efficiency of 30 InDel markers in four Chinese ethnic groups residing in Sichuan. Forensic Sci Res 2020; 7:498-502. [DOI: 10.1080/20961790.2020.1737470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Fei Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyuan Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mingkun Xie
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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Liu J, Ye Z, Wang Z, Zou X, He G, Wang M, Wang S, Hou Y. Genetic diversity and phylogenetic analysis of Chinese Han and Li ethnic populations from Hainan Island by 30 autosomal insertion/deletion polymorphisms. Forensic Sci Res 2019; 7:189-195. [PMID: 35784419 PMCID: PMC9245983 DOI: 10.1080/20961790.2019.1672933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
With the characteristics of low mutation rate, length variation and short amplicon size, insertion/deletion polymorphisms (InDels) have the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Herein, people of two ethnicities from Hainan Island were genotyped for the first time using the Investigator DIPplex kit. We investigated the forensic parameters of the 30 InDels and the phylogenetic relationships among different populations. The accumulated powers of discrimination and powers of exclusion were 0.999 999 999 9646 and 0.9897 in the Hainan Han population and 0.999 999 999 9292 and 0.9861 in the Hainan Li population, respectively. Additionally, population comparisons among geographically, ethnically and linguistically diverse populations via cluster heatmap, multidimensional scaling, principal component analysis, phylogenetic tree and STRUCTURE analyses demonstrated that the Hainan Han population had genetic similarities to the other Han, She and Tujia populations, while the Hainan Li population had close genetic relationships to the Zhuang and Miao groups; both populations had a high degree of genetic differentiation from most Turkic-speaking populations. Aforementioned results suggested that the 30 autosomal InDels are highly polymorphic and informative, which are suitable for human identification and population genetics. Four hundred and forty-five Chinese individuals from two ethnicities (Hainan Han and Hainan Li) were firstly analyzed by 30 autosomal InDels included in the Investigator DIPplex panel. Forensic parameters of the 30 InDels in the two populations showed high polymorphism and universality for human identification purposes. The Investigator DIPplex panel had a certain capacity of differentiating intercontinental populations and different language populations.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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11
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A comprehensive exploration of the genetic legacy and forensic features of Afghanistan and Pakistan Mongolian-descent Hazara. Forensic Sci Int Genet 2019; 42:e1-e12. [DOI: 10.1016/j.fsigen.2019.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/23/2019] [Accepted: 06/23/2019] [Indexed: 01/09/2023]
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12
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Genetic diversity, structure and forensic characteristics of Hmong-Mien-speaking Miao revealed by autosomal insertion/deletion markers. Mol Genet Genomics 2019; 294:1487-1498. [PMID: 31312894 DOI: 10.1007/s00438-019-01591-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/22/2019] [Indexed: 02/08/2023]
Abstract
Insertion/deletion (Indel) genetic markers have special features compared to other forensic-related markers, such as the low mutation rate and di-allelic markers with length polymorphism, playing an indispensable role in the forensic and population genetics, molecular anthropology and evolutionary biology. However, the genetic diversity, allelic frequency, forensic parameters and population genetic characteristics of the Indel markers in Hmong-Mien-speaking Guizhou Miao people are unclear due to the sparse sampling. Thus, we genotyped 30 forensic-related Indel markers in 311 unrelated healthy Miao individuals (149 females and 161 males) residing in the Guizhou Province in Southwest China using the Investigator DIPplex amplification system. All 30 Indels are in accordance with the no departures of Hardy-Weinberg equilibrium and linkage disequilibrium. The combined probability of discrimination and the probability of exclusion in Guizhou Miao population are 0.999999999948 and 0.9843, respectively. This observed ideal forensic parameter estimates indicate that this di-allelic Indel panel can be used as a supplementary tool in forensic retinue personal identification and complemented for autosomal STRs in the parentage testing in Miao population, especially used as the main tool in old or highly degraded samples in disaster victim identification. Eleven Indels show a high allele frequency difference between different continental populations and could be used as ancestry-informative markers in forensic ancestry inference. Phylogenetic relationships between Guizhou Miao and 68 worldwide populations based on the genetic polymorphisms of Indels are investigated via three different pairwise genetic distances, principal component analysis, multidimensional scaling analysis and phylogenetic relationship reconstructions. Analyses of the comprehensive population genetic relationship comparison reveal significant genetic differentiation of Chinese groups. Our results demonstrate that Guizhou Miao people are genetically closer related to the geographically adjacent populations, especially with Liangshan Yi, Guangxi Miao and Dong, but genetically distinct with Turkic-speaking populations. Comprehensive and precise genetic admixture and divergence history of Guizhou Miao and neighboring populations are needed to further investigate and reconstruct via high-density marker panel or whole-genome sequencing of modern or ancient Miao samples.
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13
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Du W, Feng C, Yao T, Xiao C, Huang H, Wu W, Zhu L, Qiao H, Liu C, Chen L. Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations. PeerJ 2019; 7:e6861. [PMID: 31110924 PMCID: PMC6501771 DOI: 10.7717/peerj.6861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
Aim In this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application. Result No deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region. Conclusion This study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations.
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Affiliation(s)
- Weian Du
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Guangdong Homy Genetics Incorporation, Foshan, China
| | - Chunlei Feng
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Ting Yao
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Cheng Xiao
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Hongyan Huang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Weibin Wu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Linnan Zhu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Honghua Qiao
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Guangzhou Forensic Science Institute, Guangzhou, China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
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14
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Chen L, Du W, Wu W, Yu A, Pan X, Feng P, Feng C, Li C, Xu L, Liu C, Liu C. Developmental validation of a novel six-dye typing system with 47 A-InDels and 2 Y-InDels. Forensic Sci Int Genet 2019; 40:64-73. [DOI: 10.1016/j.fsigen.2019.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/17/2018] [Accepted: 02/10/2019] [Indexed: 10/27/2022]
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15
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Li L, Ye Y, Song F, Wang Z, Hou Y. Genetic structure and forensic parameters of 30 InDels for human identification purposes in 10 Tibetan populations of China. Forensic Sci Int Genet 2019; 40:e219-e227. [PMID: 30744985 DOI: 10.1016/j.fsigen.2019.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/02/2019] [Accepted: 02/03/2019] [Indexed: 01/21/2023]
Abstract
Insertion/deletion analysis can serve as a promising and useful supporting tool in forensic research. The Qiagen Investigator® DIPplex Kit contained 30 well-chosen autosomal InDels was targeted to reveal the population genetic variation. In the present study, 10 Tibetan populations residing in different geographic areas of China were recruited and genotyped by Investigator® DIPplex Kit. Allele frequencies and forensic parameters were determined. No significant departures from Hard-Weinberg equilibrium (HWE) in all loci/populations after Bonferroni correction. The combined matching probability values range from 1.7148 × 10-11 to 5.3516 × 10-1° in 10 Tibetan populations. Our results revealed 10 Tibetan populations in China are genetically very similar. Intercontinental population differentiation analysis indicated Tibetan populations had a close genetic relationship with East Asian populations using Hierarchical clustering, multi-dimensional scaling (MDS), principal component analysis (PCA) and STRUCTURE. Comprehensive population genetic studies revealed that the 30-InDels assay was similarly efficient in forensic personal identification and could be regarded as an effective supplementary protocol for kinship testing.
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Affiliation(s)
- Luyao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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16
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Xie T, Guo Y, Chen L, Fang Y, Tai Y, Zhou Y, Qiu P, Zhu B. A set of autosomal multiple InDel markers for forensic application and population genetic analysis in the Chinese Xinjiang Hui group. Forensic Sci Int Genet 2018; 35:1-8. [PMID: 29602069 DOI: 10.1016/j.fsigen.2018.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/01/2018] [Accepted: 03/12/2018] [Indexed: 01/01/2023]
Abstract
In recent years, insertion/deletion (InDel) markers have become a promising and useful supporting tool in forensic identification cases and biogeographic research field. In this study, 30 InDel loci were explored to reveal the genetic diversities and genetic relationships between Chinese Xinjiang Hui group and the 25 previously reported populations using various biostatistics methods such as forensic statistical parameter analysis, phylogenetic reconstruction, multi-dimensional scaling, principal component analysis, and STRUCTURE analysis. No deviations from Hardy-Weinberg equilibrium tests were found at all 30 loci in the Chinese Xinjiang Hui group. The observed heterozygosity and expected heterozygosity ranged from 0.1971 (HLD118) to 0.5092 (HLD92), 0.2222 (HLD118) to 0.5000 (HLD6), respectively. The cumulative probability of exclusion and combined power of discrimination were 0.988849 and 0.99999999999378, respectively, which indicated that these 30 loci could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. The results of present research based on the different methods of population genetic analysis revealed that the Chinese Xinjiang Hui group had close relationships with most Chinese groups, especially Han populations. In spite of this, for a better understanding of genetic background of the Chinese Xinjiang Hui group, more molecular genetic markers such as ancestry informative markers, single nucleotide polymorphisms (SNPs), and copy number variations will be conducted in future studies.
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Affiliation(s)
- Tong Xie
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Ling Chen
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yunchun Tai
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yongsong Zhou
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Pingming Qiu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
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17
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A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures. Biochem Biophys Res Commun 2018; 497:591-596. [PMID: 29448110 DOI: 10.1016/j.bbrc.2018.02.109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 02/11/2018] [Indexed: 11/22/2022]
Abstract
Unbalanced DNA mixture is still a difficult problem for forensic practice. DIP-STRs are useful markers for detection of minor DNA but they are not widespread in the human genome and having long amplicons. In this study, we proposed a novel type of genetic marker, termed DIP-SNP. DIP-SNP refers to the combination of INDEL and SNP in less than 300bp length of human genome. The multiplex PCR and SNaPshot assay were established for 14 DIP-SNP markers in a Chinese Han population from Shanxi, China. This novel compound marker allows detection of the minor DNA contributor with sensitivity from 1:50 to 1:1000 in a DNA mixture of any gender with 1 ng-10 ng DNA template. Most of the DIP-SNP markers had a relatively high probability of informative alleles with an average I value of 0.33. In all, we proposed DIP-SNP as a novel kind of genetic marker for detection of minor contributor from unbalanced DNA mixture and established the detection method by associating the multiplex PCR and SNaPshot assay. DIP-SNP polymorphisms are promising markers for forensic or clinical mixture examination because they are shorter, widespread and higher sensitive.
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