1
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Identification of missing persons through kinship analysis by microhaplotype sequencing of single-source DNA and two-person DNA mixtures. Forensic Sci Int Genet 2022; 58:102689. [DOI: 10.1016/j.fsigen.2022.102689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/22/2022] [Accepted: 03/14/2022] [Indexed: 11/04/2022]
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2
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Screening of highly discriminative microhaplotype markers for individual identification and mixture deconvolution in East Asian populations. Forensic Sci Int Genet 2022; 59:102720. [DOI: 10.1016/j.fsigen.2022.102720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/23/2022]
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3
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Wu R, Chen H, Li R, Zang Y, Shen X, Hao B, Wang Q, Sun H. Pairwise kinship testing with microhaplotypes: Can advancements be made in kinship inference with these markers? Forensic Sci Int 2021; 325:110875. [PMID: 34166816 DOI: 10.1016/j.forsciint.2021.110875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Kinship testing based on genetic relatedness is one of the major tasks in forensic genetics. Although short tandem repeats (STRs) are the "gold standard" biomarkers for relationship testing, microhaplotypes (MHs) have also emerged as viable options for kinship elucidation. In this work, the kinship testing efficiency of 54 highly polymorphic MHs was studied in two extended families consisting of parent-offspring, full siblings, grandparent-grandchildren, uncle/aunt-nephew/nieces, and first cousins. In addition, ten-thousand pairs of different degrees of relationships were simulated using various datasets including 54 MHs, 27 STRs plus 94 single nucleotide polymorphisms (SNPs) that were included in the ForenSeq DNA Signature Prep Kit (ForenSeq), 54 MHs plus loci in ForenSeq, and different subsets of 417-published MHs. The panels' system effectiveness in the kinship analysis were accessed by likelihood ratio distributions. The results showed that 54 MHs could be used in first-degree relationship testing with high reliability. The effectiveness of 54 MHs was slightly lower than ForenSeq but only by a narrow margin. Both 54 MHs and ForenSeq were not sufficient for distant relationship testing, and approximately 200 microhaplotypes with an average expected heterozygosity (He) = 0.79 were enough to determine second-degree relationships, but a panel of 417 MHs with an average He = 0.72 was not sufficient to first cousins testing according to the simulation analysis. In conclusion, 54 MHs could be used to serve as supplement markers for kinship testing; and well-established STR markers plus well-performing microhaplotype markers may become collective tools in forensic applications, though an enlarged pool of forensic markers is needed for distant relationship testing.
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Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Hui Chen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Yu Zang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Bo Hao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
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4
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Zhang Y, Wang S, He H, Wang X, Zhu D, Wen X, Zhang S. Evaluation of three microhaplotypes in individual identification and ancestry inference. Forensic Sci Int 2021; 320:110681. [PMID: 33549990 DOI: 10.1016/j.forsciint.2021.110681] [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: 11/11/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
Microhaplotype as an emerging genetic marker has attracted more attention in forensic field. The purpose of this study was to evaluate the potential of microhaplotypes in individual identification and ancestry inference in Chinese Hainan Li and 26 1000 G populations. Three microhaplotypes were genotyped from 100 Li individuals using Agena MassARRAY. Moreover, 2504 individuals from 26 populations (1000 Genomes Project database) were enrolled. The genotypes frequencies of microhaplotypes in each population were calculated by the Plink software. We used Structure, Arlequin, and MEGA6 software to analyze the genetic structure, differentiation and genetic background difference, respectively. The forensic parameters of these microhaplotypes were calculated using Modified Powerstats software. The distribution of genotypes frequencies of three microhaplotypes elaborated the high diversities among the Li and 26 1000 G populations. Li population had a close genetic relationship with EAS populations using structure analysis. No differentiation was observed between Li and CHS population by Fst analysis. The NJ tree showed that the genetic background of Li and CHS is most similar. The average heterozygosity (HE), probability of match (PM), power of discrimination (PD), probability of exclusion (PE) and polymorphism information content (PIC) values for the three microhaplotypes in 27 populations were 0.535, 0.497, 0.465, 0.325, and 0.481, respectively. In conclusion, our results revealed three microhaplotypes as individual identification and ancestry inference genetic markers among Li population and 26 1000 G populations. Future studies are needed to confirm our results with larger samples and select much higher forensic efficacy microhaplotypes.
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Affiliation(s)
- Yingai Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Shunlan Wang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Haowei He
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Xianwen Wang
- Criminal Technical Detachment, Haikou City Public Security Bureau, Haikou, Hainan, 570208, China
| | - Dan Zhu
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Xiaohong Wen
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Shufang Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China.
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5
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Standage DS, Mitchell RN. MicroHapDB: A Portable and Extensible Database of All Published Microhaplotype Marker and Frequency Data. Front Genet 2020; 11:781. [PMID: 32849792 PMCID: PMC7427474 DOI: 10.3389/fgene.2020.00781] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/30/2020] [Indexed: 02/03/2023] Open
Abstract
Microhaplotypes are the subject of significant interest in the forensics community as a promising multi-purpose forensic DNA marker for human identification. Microhaplotype markers are composed of multiple SNPs in close proximity, such that a single NGS read can simultaneously genotype the individual SNPs and phase them in aggregate to determine the associated donor haplotype. Abundant throughout the human genome, numerous recent studies have sought to discover and rank microhaplotype markers according to allelic diversity within and among populations. Microhaplotypes provide an appealing alternative to STR markers for human identification and mixture deconvolution, but can also be optimized for ancestry inference or combined with phenotype SNPs for prediction of externally visible characteristics in a multiplex NGS assay. Designing and evaluating panels of microhaplotypes is complicated by the lack of a convenient database of all published data, as well as the lack of population allele frequency data spanning disparate marker collections. We present MicroHapDB, a comprehensive database of published microhaplotype marker and frequency data, as a tool to advance the development of microhaplotype-based human forensics capabilities. We also present population allele frequencies derived from 26 global population samples for all microhaplotype markers published to date, facilitating the design and interpretation of custom multi-source panels. We submit MicroHapDB as a resource for community members engaged in marker discovery, population studies, assay development, and panel and kit design.
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Affiliation(s)
- Daniel S Standage
- National Bioforensic Analysis Center, National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, United States
| | - Rebecca N Mitchell
- National Bioforensic Analysis Center, National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, United States
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6
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Zhang R, Tan Y, Jian H, Qu S, Liu Y, Zhu J, Wang L, Lv M, Liao M, Zhang L, Yang F, Liang W. A new approach to detect a set of SNP-SNP markers: Combining ARMS-PCR with SNaPshot technology. Electrophoresis 2020; 41:1189-1197. [PMID: 32333411 DOI: 10.1002/elps.202000009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/10/2020] [Accepted: 04/17/2020] [Indexed: 12/28/2022]
Abstract
Microhaplotypes are a new promising type of forensic genetic marker. Without the interference of stutter and high mutation rates as for STRs, and with short amplification lengths and a higher degree of polymorphism than single SNP, microhaplotypes composed of two SNPs, SNP-SNP, have a strong application potential. Currently, the most common method to detect microhaplotypes is massive parallel sequencing. However, the cost and extensive use of instruments limit its wide application in forensic laboratories. In this study, we screened 23 new SNP-SNP loci and established a new detection method by combining a multiplex amplification refractory mutation system-based PCR (ARMS-PCR) and SNaPshot technology based on CE. First, we introduced an additional deliberate mismatch at the antepenultimate base from the 3' end of primers when designing ARMS-PCR for SNP 1 (the first SNP of the SNP-SNP). Then, single base extension primers for SNaPshot assay were designed next to the position of SNP 2 (the second SNP). Finally, 15 loci were successfully built into four panels and these loci showed a relatively high level of polymorphism in the Southwest Chinese Han population. All the loci had an average probability of informative genotypes (I value) of 0.319 and a combined discrimination power of 0.999999999. Therefore, this new detection system will provide a valuable supplement to current methods.
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Affiliation(s)
- Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Hui Jian
- 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
| | - Yuqing Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jing Zhu
- Department of Forensic Science and Technology, Sichuan Police College, Luzhou, Sichuan, P. R. China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Chengdu, Sichuan, P. R. China
| | - Meili Lv
- Department of Immunology, West China School of Preclinical 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
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Fan Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Chengdu, Sichuan, P. R. China.,Department of Ultrasonography, West China Second University Hospital, 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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7
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Pang JB, Rao M, Chen QF, Ji AQ, Zhang C, Kang KL, Wu H, Ye J, Nie SJ, Wang L. A 124-plex Microhaplotype Panel Based on Next-generation Sequencing Developed for Forensic Applications. Sci Rep 2020; 10:1945. [PMID: 32029845 PMCID: PMC7004988 DOI: 10.1038/s41598-020-58980-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/23/2020] [Indexed: 11/09/2022] Open
Abstract
Microhaplotypes are an emerging type of forensic genetic marker that are expected to support multiple forensic applications. Here, we developed a 124-plex panel for microhaplotype genotyping based on next-generation sequencing (NGS). The panel yielded intralocus and interlocus balanced sequencing data with a high percentage of effective reads. A full genotype was determined with as little as 0.1 ng of input DNA. Parallel mixture experiments and in-depth comparative analyses were performed with capillary-electrophoresis-based short tandem repeat (STR) and NGS-based microhaplotype genotyping, and demonstrated that microhaplotypes are far superior to STRs for mixture deconvolution. DNA from Han Chinese individuals (n = 256) was sequenced with the 124-plex panel. In total, 514 alleles were observed, and the forensic genetic parameters were calculated. A comparison of the forensic parameters for the 20 microhaplotypes with the top Ae values in the 124-plex panel and 20 commonly used forensic STRs showed that these microhaplotypes were as effective as STRs in identifying individuals. A linkage disequilibrium analysis showed that 106 of the 124 microhaplotypes were independently hereditary, and the combined match probability for these 106 microhaplotypes was 5.23 × 10-66. We conclude that this 124-plex microhaplotype panel is a powerful tool for forensic applications.
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Affiliation(s)
- Jing-Bo Pang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China
| | - Min Rao
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China
| | - Qing-Feng Chen
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China
| | - Chi Zhang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
| | - Hao Wu
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China.
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China.
| | - Sheng-Jie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China.
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China.
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China.
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8
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Zhang C, Cao YD, Song JJ, Rao M, Nie SJ, Zhang GF, Kang KL, Ji AQ, Ye J, Wang L. MHTyper: a microhaplotype allele-calling pipeline for use with next generation sequencing data. AUST J FORENSIC SCI 2019. [DOI: 10.1080/00450618.2019.1699956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Chi Zhang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | | | - Jiao-Jiao Song
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - Min Rao
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, PR China
- Forensic Science Institute of Zhongshan Municipal Public Security Bureau, Zhongshan, Guangdong, PR China
| | - Sheng-Jie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, PR China
| | - Guang-Feng Zhang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
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9
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Building a custom large-scale panel of novel microhaplotypes for forensic identification using MiSeq and Ion S5 massively parallel sequencing systems. Forensic Sci Int Genet 2019; 45:102213. [PMID: 31835179 DOI: 10.1016/j.fsigen.2019.102213] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
A large number of new microhaplotype loci were identified in the human genome by applying a directed search with selection criteria emphasizing short haplotype length (<120 nucleotides) and maximum levels of polymorphism in the composite SNPs. From these searches, 107 autosomal microhaplotypes and 11 X chromosome microhaplotypes were selected, with well-spaced autosomal positions to ensure their independence in relationship tests. The 118 microhaplotypes were assembled into a single multiplex assay for the analysis of forensic DNA with massively parallel sequencing (MPS). A single AmpliSeq-adapted primer set was made for Illumina MiSeq and Thermo Fisher Ion S5 MPS platforms and the performance of the assay was comprehensively evaluated in both systems. Five microhaplotypes showed critical sequencing failures in both MPS platforms and were removed, while a further 13 required manual checks and the application of sequence quality thresholds in one or both systems to ensure the successful analysis of low-level DNA in these loci. The targeting of short microhaplotype spans during marker selection, with an average length of 51 nucleotides in the 118 loci, led to a high level of sensitivity for the panel when sequencing the very degraded DNA typically encountered in forensic casework and the identification of missing persons.
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10
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Phillips C, McNevin D, Kidd K, Lagacé R, Wootton S, de la Puente M, Freire-Aradas A, Mosquera-Miguel A, Eduardoff M, Gross T, Dagostino L, Power D, Olson S, Hashiyada M, Oz C, Parson W, Schneider P, Lareu M, Daniel R. MAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations. Forensic Sci Int Genet 2019; 42:213-226. [DOI: 10.1016/j.fsigen.2019.06.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 11/25/2022]
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11
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Zhu J, Lv M, Zhou N, Chen D, Jiang Y, Wang L, He W, Peng D, Li Z, Qu S, Wang Y, Wang H, Luo H, An G, Liang W, Zhang L. Genotyping polymorphic microhaplotype markers through the Illumina® MiSeq platform for forensics. Forensic Sci Int Genet 2019; 39:1-7. [DOI: 10.1016/j.fsigen.2018.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 10/07/2018] [Accepted: 11/06/2018] [Indexed: 01/09/2023]
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12
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Oldoni F, Kidd KK, Podini D. Microhaplotypes in forensic genetics. Forensic Sci Int Genet 2018; 38:54-69. [PMID: 30347322 DOI: 10.1016/j.fsigen.2018.09.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 01/28/2023]
Abstract
Microhaplotype loci (microhaps, MHs) are a novel type of molecular marker of less than 300 nucleotides, defined by two or more closely linked SNPs associated in multiple allelic combinations. The value of these markers is enhanced by massively parallel sequencing (MPS), which allows the sequencing of both parental haplotypes at each of the many multiplexed loci. This review describes the features of these multi-SNP markers and documents their value in forensic genetics, focusing on individualization, biogeographic ancestry inference, and mixture deconvolution. Foreseeable applications also include missing person identification, relationship testing, and medical diagnostic applications. The technique is not restricted to humans.
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Affiliation(s)
- Fabio Oldoni
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States
| | - Kenneth K Kidd
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT, 06520, United States
| | - Daniele Podini
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States.
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13
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Mo SK, Ren ZL, Yang YR, Liu YC, Zhang JJ, Wu HJ, Li Z, Bo XC, Wang SQ, Yan JW, Ni M. A 472-SNP panel for pairwise kinship testing of second-degree relatives. Forensic Sci Int Genet 2018; 34:178-185. [PMID: 29510334 DOI: 10.1016/j.fsigen.2018.02.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/22/2018] [Accepted: 02/25/2018] [Indexed: 10/17/2022]
Abstract
Kinship testing based on genetic markers, as forensic short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), has valuable practical applications. Paternity and first-degree relationship can be accurately identified by current commonly-used forensic STRs and reported SNP markers. However, second-degree and more distant relationships remain challenging. Although ∼105-106 SNPs can be used to estimate relatedness of higher degrees, genome-wide genotyping and analysis may be impractical for forensic use. With rapid growth of human genome data sets, it is worthwhile to explore additional markers, especially SNPs, for kinship analysis. Here, we reported an autosomal SNP panel consisted of 342 SNP selected from >84 million SNPs and 131 SNPs from previous systems. We genotyped these SNPs in 136 Chinese individuals by multiplex amplicon Massively Parallel Sequencing, and performed pairwise gender-independent kinship testing. The specificity and sensitivity of these SNPs to distinguish second-degree relatives and the unrelated was 99.9% and 100%, respectively, compared with 53.7% and 99.9% of 19 commonly-used forensic STRs. Moreover, the specificity increased to 100% by the combined use of these STRs and SNPs. The 472-SNP panel could also greatly facilitate the discrimination among different relationships. We estimated that the power of ∼6.45 SNPs were equivalent to one forensic STR in the scenario of 2nd-degree relative pedigree. Altogether, we proposed a panel of 472 SNP markers for kinship analysis, which could be important supplementary of current forensic STRs to solve the problem of second-degree relative testing.
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Affiliation(s)
- Shao-Kang Mo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China; Department of Reproductive Center, General Hospital of Lanzhou Military Region, Lanzhou 730050, China.
| | - Zi-Lin Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Ya-Ran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ya-Cheng Liu
- Department of Genetics, Beijing Tongda Shoucheng Institute of Forensic Science, Beijing 100192, China.
| | - Jing-Jing Zhang
- Department of Biotechnology, Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Hui-Juan Wu
- Department of Biotechnology, Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Zhen Li
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Xiao-Chen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Sheng-Qi Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Jiang-Wei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ming Ni
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
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Construction and forensic genetic characterization of 11 autosomal haplotypes consisting of 22 tri-allelic indels. Forensic Sci Int Genet 2018; 34:71-80. [PMID: 29428890 DOI: 10.1016/j.fsigen.2018.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 01/20/2018] [Accepted: 02/01/2018] [Indexed: 01/22/2023]
Abstract
Insertion/deletion polymorphisms (indels), which combine the advantages of both short tandem repeats and single-nucleotide polymorphisms, are suitable for parentage testing. To overcome the limitations of the low polymorphism of di-allelic indels, we constructed a set of haplotypes with physically linked, multi-allelic indels. Candidate haplotypes were selected from the 1000 Genomes Project database, and were subject to the following criteria for inclusion: (i) each marker must have a minimum allele frequency (MAF) of ≥0.1 in the Han population of China; (ii) markers must exist in a non-coding region; (iii) the physical distance between a pair of candidate indels must be <500 bp; (iv) the allele length variation of each indel from 1 to 20 bp; (v) different haplotypes must be located on different chromosomes or chromosomal arms, or be more than 10 Mb apart if on the same chromosomal arm; and (vi) they must not be located across a recombination hotspot. A multiplex system with 11 haplotype markers, comprising 22 tri-allelic indel loci distributed over 10 chromosomes was developed. To validate the multiplex panel, we investigated the haplotype distribution in sets of two and three-generation pedigrees. The results demonstrated that the haplotypes consisting of multi-allelic indel markers exhibited higher polymorphism than a single indel locus, and thus provide Supplementary information for forensic kinship identification.
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Laurent FX, Vibrac G, Rubio A, Thévenot MT, Pène L. [The future of forensic DNA analysis for criminal justice]. Med Sci (Paris) 2017; 33:971-978. [PMID: 29200395 DOI: 10.1051/medsci/20173311014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the criminal framework, the analysis of approximately 20 DNA microsatellites enables the establishment of a genetic profile with a high statistical power of discrimination. This technique gives us the possibility to establish or exclude a match between a biological trace detected at a crime scene and a suspect whose DNA was collected via an oral swab. However, conventional techniques do tend to complexify the interpretation of complex DNA samples, such as degraded DNA and mixture DNA. The aim of this review is to highlight the powerness of new forensic DNA methods (including high-throughput sequencing or single-cell sequencing) to facilitate the interpretation of the expert with full compliance with existing french legislation.
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Affiliation(s)
- François-Xavier Laurent
- Institut national de police scientifique, laboratoire de police scientifique de Lyon, 31, avenue Franklin Roosevelt, 69134 Écully Cedex, France
| | - Geoffrey Vibrac
- Université de Lorraine, Institut François Gény - Institut de Sciences criminelles et de Droit médical (EA 7301), 13, place Carnot, 54000 Nancy, France
| | - Aurélien Rubio
- Cour d'appel de Nancy, 3, rue Suzanne Regnault-Gousset, 54000 Nancy, France
| | - Marie-Thérèse Thévenot
- Institut national de police scientifique, laboratoire de police scientifique de Lyon, 31, avenue Franklin Roosevelt, 69134 Écully Cedex, France
| | - Laurent Pène
- Institut national de police scientifique, laboratoire de police scientifique de Lyon, 31, avenue Franklin Roosevelt, 69134 Écully Cedex, France
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16
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Evaluating 130 microhaplotypes across a global set of 83 populations. Forensic Sci Int Genet 2017; 29:29-37. [PMID: 28359046 DOI: 10.1016/j.fsigen.2017.03.014] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/17/2017] [Accepted: 03/12/2017] [Indexed: 01/08/2023]
Abstract
Today the primary DNA markers used in forensics are short tandem repeat (STR) polymorphisms (STRPs), initially selected because they are highly polymorphic. However, the increasingly common need to deal with samples with a mixture of DNA from two or more individuals sometimes is complicated by the inherent stutter involved with PCR amplification, especially in strongly unbalanced mixtures when the minor component coincides with the stutter range of the major component. Also, the STRPs in use provide little evidence of ancestry of a single source sample beyond broad "continental" resolution. Methodologies for analyzing DNA have become much more powerful in recent years. Massively parallel sequencing (MPS) is a new method being considered for routine use in forensics. Primarily to aid in mixture deconvolution and avoid the issue of stutter, we have begun to investigate a new type of forensic marker, microhaplotype loci, that will provide useful information on mixtures of DNA and on ancestry when typed using massively parallel sequencing (MPS). We have identified 130 loci and estimated their haplotype (allele) frequencies in 83 different population samples. Many of these loci are shown to be highly informative for individual identification and for mixture identification and deconvolution.
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17
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Chen P, Zhu J, Pu Y, Jiang Y, Chen D, Wang H, Mao J, Zhou B, Gao L, Bai P, Liang W, Zhang L. Microhaplotype identified and performed in genetic investigation using PCR-SSCP. Forensic Sci Int Genet 2017; 28:e1-e7. [PMID: 28174015 DOI: 10.1016/j.fsigen.2017.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 12/02/2016] [Accepted: 01/17/2017] [Indexed: 01/04/2023]
Abstract
The recently introduced concept of microhaplotype loci has attracted attention in forensics. Previous studies estimated the allele frequencies generally through obtaining genotypic data on the individual SNPs from a larger set of unrelated individuals then phasing microhaplotypes by statistical and computational techniques. Determining phase for a single new individual requires the larger set of individuals to have been genotyped previously. Rare microhaplotypes possessed only by the target individual or microhaplotypes private to a specific population not previously studied are unlikely to be accurately phased using data sets of SNPs. Thus, there is a demand for an approach that could directly determine a gain single individual's precise microhaplotype information. In the present study, we introduced potential approaches of single chain sequencing based Massively Parallel Sequencing Technology (MiSeq) and PCR based Single Strand Conformational Polymorphism (SSCP) technology which was simple, accurate, and cost-effective. The results indicated that microhaplotypes contain much more polymorphic information than divided SNPs per locus (average heterozygosity of microhaplotype 0.61 VS SNPs 0.41). When microhaplotype allele frequencies were compared among five Chinese ethnic populations, significantly different distributions were found between the Han and Uyghur populations. Further analysis of pairwise Fst values and analysis of molecular variance (AMOVA), showed significant population differentiation between the Uyghur and other populations.
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Affiliation(s)
- Peng Chen
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Jing Zhu
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Yan Pu
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Youjing Jiang
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Dan Chen
- Department of Forensic Genetics, Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu 610081, Sichuan, PR China
| | - Hui Wang
- Department of Forensic Genetics, Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu 610081, Sichuan, PR China
| | - Jiong Mao
- Department of Forensic Genetics, Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu 610081, Sichuan, PR China
| | - Bin Zhou
- Laboratory of Molecular Translational Medicine, West China Institute of Women and Children's Health, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China
| | - Linbo Gao
- Laboratory of Molecular Translational Medicine, West China Institute of Women and Children's Health, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China
| | - Peng Bai
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Weibo Liang
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China.
| | - Lin Zhang
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Laboratory of Molecular Translational Medicine, West China Institute of Women and Children's Health, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China.
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18
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Abstract
Microhaplotypes are a new type of genetic marker in forensics and population genetics. A standardized nomenclature is desirable. A simple approach that does not require a central authority for approval is proposed. The nomenclature proposed follows the recommendation of the HUGO Gene Nomenclature Committee ( http://www.genenames.org ): "We strongly encourage naming families and groups of genes related by sequence and/or function using a "root" symbol. This is an efficient and informative way to name related genes, and already works well for a number of established gene families…" The proposal involves a simple root consisting of "mh" followed by the two-digit chromosome number and unique characters established by the authors in the initial publication. We suggest the unique symbol be an indication of the laboratory followed by characters unique to the chromosome and laboratory. For instance, the microhaplotype symbol mh01KK-001 refers to a locus on chromosome 1 published by the Kidd Lab (KK-) as their #001. Publication defines mh01KK-001 as comprised of four single nucleotide polymorphisms (SNPs), rs4648344, rs6663840, rs58111155, and rs6688969.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA.
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Analysis of Short Tandem Repeat and Single Nucleotide Polymorphism Loci From Single-Source Samples Using a Custom HaloPlex Target Enrichment System Panel. Am J Forensic Med Pathol 2016; 37:99-107. [DOI: 10.1097/paf.0000000000000228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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A Genome-Wide Scan of DNA Methylation Markers for Distinguishing Monozygotic Twins. Twin Res Hum Genet 2015; 18:670-9. [PMID: 26500037 DOI: 10.1017/thg.2015.73] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Identification of individuals within pairs of monozygotic (MZ) twins remains unresolved using common forensic DNA typing technology. For some criminal cases involving MZ twins as suspects, the twins had to be released due to inability to identify which of the pair was the perpetrator. In this study, we performed a genome-wide scan on whole blood-derived DNA from four pairs of healthy phenotypically concordant MZ twins using the methylated DNA immunoprecipitation sequencing technology to identify candidate DNA methylation markers with capacity to distinguish MZ twins within a pair. We identified 38 differential methylation regions showing within-pair methylation differences in all four MZ pairs. These are all located in CpG islands, 17 of which are promoter-associated, 17 are intergenic islands, and four are intragenic islands. Genes associated with these markers are related with cell proliferation, differentiation, and growth and development, including zinc finger proteins, PRRX2, RBBP9, or are involved in G-protein signaling, such as the regulator of G-protein signaling 16. Further validation studies on additional MZ twins are now required to evaluate the broader utility of these 38 markers for forensic use.
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