1
|
Lan Q, Cai M, Xu H, Bai X, Shen C, Zhu B. Developmental validation of a custom-designed Multi-InDel panel: A five-dye multiplex amplification system for challenging DNA samples. Electrophoresis 2024; 45:489-504. [PMID: 38037290 DOI: 10.1002/elps.202300192] [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: 08/29/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
The continual investigation of novel genetic markers has yielded promising solutions for addressing the challenges encountered in forensic DNA analysis. In this study, we have introduced a custom-designed panel capable of simultaneously amplifying 41 novel Multi-insertion/deletion (Multi-InDel) markers and an amelogenin locus using the capillary electrophoresis platform. Through a developmental validation study conducted in accordance with guidelines recommended by the Scientific Working Group on DNA Analysis Methods, we demonstrated that the new Multi-InDel system exhibited the sensitivity to produce reliable genotyping profiles with as little as 62.5 pg of template DNA. Accurate and complete genotyping profiles could be obtained even in the presence of specific concentrations of PCR inhibitors. Furthermore, the maximum amplicon size for this system was limited to under 220 bp in the genotyping profile, resulting in its superior efficiency compared to commercially available short tandem repeat kits for both naturally and artificially degraded samples. In the context of mixed DNA analysis, the Multi-InDel system was proved informative in the identification of two-person DNA mixture, even when the template DNA of the minor contributor was as low as 50 pg. In conclusion, a series of performance evaluation studies have provided compelling evidence that the new Multi-InDel system holds promise as a valuable tool for forensic DNA analysis.
Collapse
Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Xiaole Bai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chunmei Shen
- Department of Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, P. R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, P. R. China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Xue J, Tan M, Zhang R, Chen D, Liu G, Zheng Y, Wu Q, Xiao Y, Liao M, Qu S, Liang W. Evaluation of microhaplotype panels for complex kinship analysis using massively parallel sequencing. Forensic Sci Int Genet 2023; 65:102887. [PMID: 37209601 DOI: 10.1016/j.fsigen.2023.102887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/22/2023]
Abstract
In recent years, microhaplotypes (MHs) have become a research hotspot within the field of forensic genetics. Traditional MHs contain only SNPs that are closely linked within short fragments. Herein, we broaden the concept of general MHs to include short InDels. Complex kinship identification plays an important role in disaster victim identification and criminal investigations. For distant relatives (e.g., 3rd-degree), many genetic markers are required to enhance power of kinship testing. We performed genome-wide screening for new MH markers composed of two or more variants (InDel or SNP) within 220 bp based on the Chinese Southern Han from the 1000 Genomes Project. An NGS-based 67plex MH panel (Panel B) was successfully developed, and 124 unrelated individual samples were sequenced to obtain population genetic data, including alleles and allele frequencies. Of the 67 genetic markers, 65 MHs were, as far as we know, newly discovered, and 32 MHs had effective number of allele (Ae) values greater than 5.0. The average Ae and heterozygosity of the panel were 5.34 and 0.7352, respectively. Next, 53 MHs from a previous study were collected as Panel A (average Ae of 7.43), and Panel C with 87 MHs (average Ae of 7.02) was formed by combining Panels A and B. We investigated the utility of these three panels in kinship analysis (parent-child, full siblings, 2nd-degree, 3rd-degree, 4th-degree, and 5th-degree relatives), with Panel C exhibiting better performance than the two other panels. Panel C was able to separate parent-child, full-sibling, and 2nd-degree relative duos from unrelated controls in real pedigree data, with a small false testing level (FTL) of 0.11% in simulated 2nd-degree duos. For more distant relationships, the FTL was much higher: 8.99% for 3rd-degree, 35.46% for 4th-degree, and 61.55% for 5th-degree. When a carefully chosen extra relative was known, this may enhance the testing power for distant kinship analysis. Two twins from the Q family (2-5 and 2-7) and W family (3-18 and 3-19) shared the same genotypes in all tested MHs, which led to the incorrect conclusion that an uncle-nephew duo was classified as a parent-child duo. In addition, Panel C showed great capacity for excluding close relatives (2nd-degree and 3rd-degree relatives) during paternity tests. Among 18,246 real and 10,000 simulated unrelated pairs, none were misinterpreted as a relative within 2nd-degree at a log10(LR) cutoff of 4. The panels presented herein could provide supplementary power for the analysis of complex kinship.
Collapse
Affiliation(s)
- Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
| |
Collapse
|
4
|
Chen M, Cui W, Bai X, Fang Y, Yao H, Zhang X, Lei F, Zhu B. Comprehensive evaluations of individual discrimination, kinship analysis, genetic relationship exploration and biogeographic origin prediction in Chinese Dongxiang group by a 60-plex DIP panel. Hereditas 2023; 160:14. [PMID: 36978173 PMCID: PMC10052841 DOI: 10.1186/s41065-023-00271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Dongxiang group, as an important minority, resides in Gansu province which is located at the northwest China, forensic detection system with more loci needed to be studied to improve the application efficiency of forensic case investigation in this group. METHODS A 60-plex system including 57 autosomal deletion/insertion polymorphisms (A-DIPs), 2 Y chromosome DIPs (Y-DIPs) and the sex determination locus (Amelogenin) was explored to evaluate the forensic application efficiencies of individual discrimination, kinship analysis and biogeographic origin prediction in Gansu Dongxiang group based on the 60-plex genotype results of 233 unrelated Dongxiang individuals. The 60-plex genotype results of 4582 unrelated individuals from 33 reference populations in five different continents were also collected to analyze the genetic background of Dongxiang group and its genetic relationships with other continental populations. RESULTS The system showed high individual discrimination power, as the cumulative power of discrimination (CPD), cumulative power of exclusion (CPE) for trio and cumulative match probability (CMP) values were 0.99999999999999999999997297, 0.999980 and 2.7029E- 24, respectively. The system could distinguish 98.12%, 93.78%, 82.18%, 62.35% and 39.32% of full sibling pairs from unrelated individual pairs, when the likelihood ratio (LR) limits were set as 1, 10, 100, 1000 and 10,000 based on the simulated family samples, respectively. Additionally, Dongxiang group had the close genetic distances with populations in East Asia, especially showed the intimate genetic relationships with Chinese Han populations, which were concluded from the genetic affinities and genetic background analyses of Dongxiang group and 33 reference populations. In terms of the effectiveness of biogeographic origin inference, different artificial intelligent algorithms possessed different efficacies. Among them, the random forest (RF) and extreme gradient boosting (XGBoost) algorithm models could accurately predict the biogeographic origins of 99.7% and 90.59% of three and five continental individuals, respectively. CONCLUSION This 60-plex system had good performance for individual discrimination, kinship analysis and biogeographic origin prediction in Dongxiang group, which could be used as a powerful tool for case investigation.
Collapse
Affiliation(s)
- Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiaole Bai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yating Fang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230031, Anhui, China
| | - Hongbin Yao
- Belt and Road Research Center for Forensic Molecular Anthropology, Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, 730070, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, 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.
| |
Collapse
|
5
|
Lan Q, Cai M, Lei F, Shen C, Zhu B. Systematically exploring the performance of a self-developed Multi-InDel system in forensic identification, ancestry inference and genetic structure analysis of Chinese Manchu and Mongolian groups. Forensic Sci Int 2023; 346:111637. [PMID: 36934684 DOI: 10.1016/j.forsciint.2023.111637] [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: 01/08/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/14/2023]
Abstract
The insertion/deletion (InDel) polymorphism has promising applications in forensic DNA analysis. However, the insufficient forensic efficiencies of the present InDel-based systems restrict their applications in parentage testing, due to the lower genetic polymorphism of the biallelic InDel locus and the limited number of InDel loci in a multiplex amplification system. Here, we introduced an in-house developed system which contained 41 polymorphic Multi-InDel markers (equivalent to 82 InDels in total), to serve as an efficient and reliable tool for different forensic applications in the Manchu and Mongolian groups. We demonstrated that the new system exhibited potential efficiencies for personal identification, parentage testing, two-person DNA mixture interpretation and ancestry inference of intercontinental populations. Meanwhile, we explored the genetic backgrounds of the Manchu and Mongolian groups by conducting a series of population genetic analyses. We showed that the Manchu and Mongolian groups shared closer genetic relationships with East Asian populations, especially Han Chinese populations in northern China. Moreover, more similar genetic compositions were detected between the Manchu group and the northern Han populations in this study, suggesting that the Manchu group had higher genetic affinities with northern Han populations than the Mongolian group. Overall. this study provided the necessary evidence that these Multi-InDel genetic markers could play an important role in forensic applications.
Collapse
Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515 Guangzhou, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515 Guangzhou, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515 Guangzhou, China
| | - Chunmei Shen
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515 Guangzhou, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.
| |
Collapse
|
6
|
State of the Art for Microhaplotypes. Genes (Basel) 2022; 13:genes13081322. [PMID: 35893059 PMCID: PMC9329722 DOI: 10.3390/genes13081322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. The random match Probability (RMP) can be as small as 10−100 for a large panel of microhaplotypes. It is possible to measure the heterozygosity of an MH as the effective number of alleles (Ae). Ae > 7.5 exists for African populations and >4.5 exists for Native American populations for a smaller panel of two dozen selected microhaplotypes. Using STRUCTURE, at least 10 different ancestral clusters can be defined by microhaplotypes. The Ae for a locus is also identical to the Paternity Index (PI), the measure of how informative a locus will be in parentage testing. High Ae loci can also be useful in missing persons cases. Finally, high Ae microhaplotypes allow the near certainty of seeing multiple additional alleles in a mixture of two or more individuals in a DNA sample. In summary, a panel of higher Ae microhaplotypes can outperform the standard CODIS markers.
Collapse
|
7
|
Li Z, Li Y, Liu N, Yuan F, Liu F, Liu J, Yun K, Yan J, Zhang G. Typing of semen-containing mixtures using ARMS-based semen-specific CpG-InDel/STR markers. Int J Legal Med 2022; 136:1163-1176. [PMID: 35633397 DOI: 10.1007/s00414-022-02843-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
Mixed traces are common biological materials found at crime scenes, and their identification remains a significant challenge in the field of forensic genetics. In recent years, DNA methylation has been considered as a promising approach for body fluid identification, and length polymorphic loci are still the preferred markers for personal identification. In this study, we used tissue-specific CpG sites with linked insertion or deletion (InDel) or short tandem repeat (STR) markers (CpG-InDel/STR) for both body fluid and individual identification. The tissue-specific CpG loci, which were all selected from the previous reports, were analyzed using a combination of bisulfite conversion and amplification refractory mutation system-multiprimer-PCR technology. InDels or STRs, which were selected within 400 bp upstream or downstream of the semen-specific CpG loci, were analyzed using a capillary electrophoresis platform. Eventually, we successfully constructed a panel containing 17 semen-specific CpG-InDel/STR compound markers compassing 21 InDels/STRs, 3 body-fluid positive controls (vaginal secretion-, saliva-, and blood-specific CpG), and 1 gender identification locus. Using this panel, full genotyping of individuals could be obtained successfully with 50 ng DNA input. Semen stains stored at room temperature for 7 months and degraded samples that were heat treated for up to 6 h were still identified efficiently. For semen containing mixed stains, it is also useful when the semen content is as low as 3.03%. Moreover, the cumulative discrimination power of this panel is 0.9999998. In conclusion, it is a robust panel enabling the validation of both the tissue source and individual identification of semen containing mixed stains and can be employed as an alternative solution for forensic case investigation.
Collapse
Affiliation(s)
- Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Yidan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Na Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Fang Yuan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Feng Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
| |
Collapse
|
8
|
Zhou J, Wang Y, Xu E. Research progress on application of microhaplotype in forensic genetics. Zhejiang Da Xue Xue Bao Yi Xue Ban 2021; 50:777-782. [PMID: 35347913 PMCID: PMC8931617 DOI: 10.3724/zdxbyxb-2021-0180] [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: 06/29/2021] [Accepted: 10/26/2021] [Indexed: 06/14/2023]
Abstract
As a novel genetic marker, microhaplotype can be applied in the field of forensic genetics. Microhaplotype has the advantages of high polymorphism, low mutation rate, no stutter products and short amplification fragments. Microhaplotype can effectively detect mixture, and quantitatively analyze the contributors of mixture. DNA with severe fragmentation can be successfully genotyped by microhaplotype. It can be used as ancestry informative marker to effectively divide the global continental population according to genetic structure. Microhaplotype system can provide more information than traditional short tandem repeat and help to identify complex relationships. It can provide new ideas for tumor source identification, cell line identification and prenatal paternity testing. Here we review the applications of microhaplotype, intending to provide references for forensic practice.
Collapse
Affiliation(s)
- Jing Zhou
- 1. Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Wang
- 1. Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Enping Xu
- 1. Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Zhejiang University, Hangzhou 310058, China
- 2. Forensic Science Center, Zhejiang University, Hangzhou 310029, China
| |
Collapse
|
9
|
Li Z, Li J, Li Y, Liu N, Liu F, Ren J, Yun K, Yan J, Zhang G. Development of a multiplex methylation-sensitive restriction enzyme-based SNP typing system for deconvolution of semen-containing mixtures. Int J Legal Med 2021; 135:1281-1294. [PMID: 33813614 DOI: 10.1007/s00414-021-02552-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/24/2021] [Indexed: 11/30/2022]
Abstract
The identification of mixed stains has always been a difficult problem in personal identification in the forensic field. In recent years, tissue-specific methylation sites have proven to be very stable biomarkers for distinguishing tissue origin. However, it is still challenging to perform tissue source identification and individual identification simultaneously. In this study, we developed a method that uses tissue-specific methylation markers combined with single-nucleotide polymorphism (SNP) markers to detect semen from mixed biofluids and to identify individuals simultaneously. Semen-specific CpG markers were chosen from the literature and further validated utilizing methylation-sensitive restriction endonuclease (MSRE) combined with PCR technology. The neighboring SNP markers were searched in the flanking sequence of the target CpG within 400 bp, and SNP typing was then carried out through a single-base extension reaction followed by capillary electrophoresis. Eventually, a method of MSRE combined with SNaPshot that could detect 12 compound CpG-SNP markers was developed. Using this system, 10 ng of total DNA and DNA mixture with semen content up to 25% could be typed successfully. Moreover, the cumulative discrimination power of the system in the northern Chinese Han population is 0.9998. This study provides a valuable strategy for forensic practice to perform tissue origin and individual identification from mixed stains simultaneously.
Collapse
Affiliation(s)
- Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Jintao Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Yidan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Na Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Feng Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Jianbo Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
| |
Collapse
|
10
|
Hao T, Guo J, Liu J, Wang J, Liu Z, Cheng X, Li J, Ren J, Li Z, Yan J, Zhang G. Predicting human age by detecting DNA methylation status in hair. Electrophoresis 2021; 42:1255-1261. [PMID: 33629357 DOI: 10.1002/elps.202000349] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 02/07/2021] [Indexed: 12/29/2022]
Abstract
Age prediction is of great importance for criminal investigation and judicial expertise. DNA methylation status is considered a promising method to infer tissue age by virtue of age-dependent changes on methylation sites. In recent years, forensic scientists have established various models to predict the chronological age of blood, saliva, and semen based on DNA methylation status. However, hair-inferred age has not been studied in the field of forensic science. In this study, we measured the methylation statuses of potential age-related CpG sites by using the multiplex methylation SNaPshot method. A total of 10 CpG sites from the LAG3, SCGN, ELOVL2, KLF14, C1orf132, SLC12A5, GRIA2, and PDE4C genes were found to be tightly associated with age in hair follicles. A correlation coefficient above 0.7 was found for four CpG sites (cg24724428 and Chr6:11044628 in ELOVL2, cg25148589 in GRIA2, and cg07547549 in SLC12A5). Among four age-prediction models, the multiple linear regression model consisting of 10 CpG sites provided the best-fitting results, with a median absolute deviation of 3.68 years. It is feasible to obtain both human identification and age information from a single scalp hair follicle. No significant differences in methylation degree were found between different sexes, hair types, or hair colors. In conclusion, we established a method to evaluate chronological age by assessing DNA methylation status in hair follicles.
Collapse
Affiliation(s)
- Ting Hao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jiangling Guo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Xiaojuan Cheng
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jintao Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jianbo Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| |
Collapse
|