1
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González-Bao J, Mosquera-Miguel A, Casanova-Adán L, Ambroa-Conde A, Ruiz-Ramírez J, Cabrejas-Olalla A, Boullón-Cassau M, Freire-Aradas A, Rodríguez-López A, Roth C, Lagacé R, Phillips C, Lareu MV, de la Puente M. Performance comparison of a previously validated microhaplotype panel and a forensic STR panel for DNA mixture analysis. Forensic Sci Int Genet 2024; 74:103144. [PMID: 39270547 DOI: 10.1016/j.fsigen.2024.103144] [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: 03/13/2024] [Revised: 07/09/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024]
Abstract
Short Tandem Repeats (STRs) are the most widespread markers in forensic genetics. However, STR stutter peaks can mask alleles from a minor contributor when analysing mixtures, hindering the interpretation of complex profiles. In this study we compared the performance of a previously described panel of microhaplotypes (MHs), an alternative type of forensic marker, against a standard STR kit. The parameters evaluated included: capability of determining the minimum number of contributors in the mixture; percentages of allele drop-outs and drop-ins; retrieval of alleles belonging to the minor contributor, and estimation of likelihood ratio (LR) values. In addition, the capacity of EuroForMix software to estimate each donor's percentage of contribution was tested, as well as the impact on results when using manually, or automatically prepared libraries. The MH panel showed better performance than STRs for the detection of 2-contributor mixtures, but the lower degree of polymorphism per MH marker hindered the task of deconvolution with multiple contributors. MHs presented higher drop-in rates and lower drop-out rates, a higher capability to recover the minor contributor's alleles and provided higher LR values than STRs, likely due to the much higher number of loci combined in the panel. Estimations of contributor ratios using EuroForMix showed promising results and marginal differences were found in these values between manually and automatically prepared libraries. Overall, results showed that the mixture detection performance of the MH panel was better or equal to the standard forensic autosomal STR panel, indicating microhaplotypes are informative markers for this purpose.
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Affiliation(s)
- J González-Bao
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - L Casanova-Adán
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Cabrejas-Olalla
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M Boullón-Cassau
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Rodríguez-López
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - C Roth
- Human Identification Group, Thermo Fisher Scientific, Pleasanton, CA, USA
| | - R Lagacé
- Human Identification Group, Thermo Fisher Scientific, Pleasanton, CA, USA
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain; King's Forensics, Faculty of Life Sciences and Medicine, King's College, London, UK
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain.
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2
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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.
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Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 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
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3
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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.
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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.
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Zhang R, Xue J, Tan M, Chen D, Xiao Y, Liu G, Zheng Y, Wu Q, Liao M, Lv M, Qu S, Liang W. An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis. Genes (Basel) 2023; 14:genes14040865. [PMID: 37107623 PMCID: PMC10137789 DOI: 10.3390/genes14040865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform. The sizes of markers and amplicons ranged between 11–81 bp and 123–198 bp, respectively. The sensitivity was 0.25 ng, and the calling results were consistent with Sanger sequencing and the Integrative Genomics Viewer (IGV). It showed measurable polymorphism among sequenced 137 Southwest Chinese Han individuals. No significant deviations in the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were found at all MHs after Bonferroni correction. Furthermore, the specificity was 1:40 for simulated two-person mixtures, and the detection rates of highly degraded single samples and mixtures were 100% and 93–100%, respectively. Moreover, animal DNA testing was incomplete and low depth. Overall, our MPS-based 50-plex MH panel is a powerful forensic tool that provides a strong supplement and enhancement for some existing panels.
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Affiliation(s)
- Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
- West China Forensics Center, Sichuan University, No. 16, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Shengqiu Qu
- West China Forensics Center, Sichuan University, No. 16, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
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Butler JM. Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019-2022. Forensic Sci Int Synerg 2022; 6:100311. [PMID: 36618991 PMCID: PMC9813539 DOI: 10.1016/j.fsisyn.2022.100311] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.
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Affiliation(s)
- John M. Butler
- National Institute of Standards and Technology, Special Programs Office, 100 Bureau Drive, Mail Stop 4701, Gaithersburg, MD, USA
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Tao R, Yang Q, Xia R, Zhang X, Chen A, Li C, Zhang S. A sequence-based 163plex microhaplotype assay for forensic DNA analysis. Front Genet 2022; 13:988223. [PMID: 36276985 PMCID: PMC9579316 DOI: 10.3389/fgene.2022.988223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Novel genetic marker microhaplotype has led to an upsurge in forensic genetic research. This study established a 163 microhaplotype (MH) multiplex assay based on next-generation sequencing (NGS) and evaluated the assay's performance and applicability. Our results showed that the 163 MH assay was accurate, repeatable and reliable, and could distinguish between African, European-American, Southern Asia and Eastern Asia populations. Among the 163 MH makers, 48 MHs with Ae > 3.0 in China Eastern Han were selected and confirmed to be highly polymorphic, with a combined power of discrimination of 1-8.26 × 10-44 and the combined power of exclusion in duos and trios of 1-1.26 × 10-8 and 1-8.27 × 10-16, respectively. Moreover, the mixture study demonstrated the realizability of the MHs in deconvoluting mixtures with different proportions of two to five-person. In conclusion, our findings support the use of this MH assay for ancestry inference, human identification, paternity testing and mixture deconvolution in forensic research.
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Affiliation(s)
| | | | | | | | | | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
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Wen D, Xing H, Liu Y, Li J, Qu W, He W, Wang C, Xu R, Liu Y, Jia H, Zha L. The application of short and highly polymorphic microhaplotype loci in paternity testing and sibling testing of temperature-dependent degraded samples. Front Genet 2022; 13:983811. [PMID: 36226179 PMCID: PMC9549137 DOI: 10.3389/fgene.2022.983811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Paternity testing and sibling testing become more complex and difficult when samples degrade. But the commonly used genetic markers (STR and SNP) cannot completely solve this problem due to some disadvantages. The novel genetic marker microhaplotype proposed by Kidd’s research group combines the advantages of STR and SNP and is expected to become a promising genetic marker for kinship testing in degraded samples. Therefore, in this study, we intended to select an appropriate number of highly polymorphic SNP-based microhaplotype loci, detect them by the next-generation sequencing technology, analyze their ability to detect degraded samples, calculate their forensic parameters based on the collected 96 unrelated individuals, and evaluate their effectiveness in paternity testing and sibling testing by simulating kinship relationship pairs, which were also compared to 15 STR loci. Finally, a short and highly polymorphic microhaplotype panel was developed, containing 36 highly polymorphic SNP-based microhaplotype loci with lengths smaller than 100 bp and Ae greater than 3.00, of which 29 microhaplotype loci could not reject the Hardy-Weinberg equilibrium and linkage equilibrium after the Bonferroni correction. The CPD and CPE of these 29 microhaplotype loci were 1-2.96E-26 and 1-5.45E-09, respectively. No allele dropout was observed in degraded samples incubated with 100°C hot water for 40min and 60min. According to the simulated kinship analysis, the effectiveness at the threshold of 4/−4 reached 98.39% for relationship parent-child vs. unrelated individuals, and the effectiveness at the threshold of 2/−2 for relationship full-sibling vs. unrelated individuals was 93.01%, which was greater than that of 15 STR loci (86.75% for relationship parent-child vs. unrelated individuals and 81.73% for relationship full-sibling vs. unrelated individuals). After combining our 29 microhaplotype loci with other 50 short and highly polymorphic microhaplotype loci, the effectiveness values at the threshold of 2/−2 were 82.42% and 90.89% for relationship half-sibling vs. unrelated individuals and full-sibling vs. half-sibling. The short and highly polymorphic microhaplotype panel we developed may be very useful for paternity testing and full sibling testing in degraded samples, and in combination with short and highly polymorphic microhaplotype loci reported by other researchers, may be helpful to analyze more distant kinship relationships.
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Affiliation(s)
- Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Hao Xing
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Ying Liu
- Xiangya Stomatological Collage, Central South University, Changsha, China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Weifeng Qu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Wei He
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Chudong Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Ruyi Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yi Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Hongtao Jia
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
- *Correspondence: Lagabaiyila Zha,
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Evaluation of the MHSeqTyper47 kit for forensically challenging DNA samples. Forensic Sci Int Genet 2022; 61:102763. [PMID: 35939876 DOI: 10.1016/j.fsigen.2022.102763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/05/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022]
Abstract
Microhaplotypes have been highly regarded for forensic mixture DNA deconvolution because they do not experience interference from stutters in the same way as short tandem repeat markers, and they tend to be more polymorphic than single nucleotide polymorphism markers. However, forensic microhaplotype kits have not been reported. The MHSeqTyper47 kit genotypes 47 microhaplotype loci. In this study, MiSeq FGx sequencing metrics for MHSeqTyper47 were presented, and the genotyping accuracy of this kit was examined. The sensitivity of MHSeqTyper47 reached 62.5 pg, and full genotyping results were obtained from degraded DNA samples with degradation indexes ≤ 3.00. Full genotypes were obtained in the presence of 100 ng/μL tannin, 50 μM heme, 25 ng/μL humic acid, and 1.25 μg/μL indigo dye. In DNA mixture studies, a minimum of 31 loci of the minor contributor were correctly genotyped at 1:99 or 99:1 mixing ratios, with the cumulative random matching probability of these loci reaching 4.54 × 10-25. Mixing ratios could be reliably predicted from two-donor DNA mixtures based on the loci with four called alleles. Taken together, these data showed that the MHSeqTyper47 kit was effective for forensically challenging DNA analysis.
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9
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Xu Q, Wang Z, Kong Q, Wang X, Huang A, Li C, Liu X. Improving the System Power of Complex Kinship Analysis by Combining Multiple Systems. Forensic Sci Int Genet 2022; 60:102741. [DOI: 10.1016/j.fsigen.2022.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 11/04/2022]
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10
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Kidd KK, Evsanaa B, Togtokh A, Brissenden JE, Roscoe JM, Dogan M, Neophytou PI, Gurkan C, Bulbul O, Cherni L, Speed WC, Murtha M, Kidd JR, Pakstis AJ. North Asian population relationships in a global context. Sci Rep 2022; 12:7214. [PMID: 35508562 PMCID: PMC9068624 DOI: 10.1038/s41598-022-10706-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/01/2022] [Indexed: 12/20/2022] Open
Abstract
Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA.
| | - Baigalmaa Evsanaa
- Department of Nephrology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Ariunaa Togtokh
- Department of Nephrology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | - Janet M Roscoe
- Department of Medicine, University of Toronto, Toronto, ON, Canada.,The Scarborough Hospital, Toronto, ON, Canada
| | - Mustafa Dogan
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | | | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee On Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia, North Cyprus, Turkey.,Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta, North Cyprus, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Science, Istanbul University, Cerrahpasa, 34500, Istanbul, Turkey
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,Higher Institute of Biotechnology of Monastir, Monastir University, 5000, Monastir, Tunisia
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Michael Murtha
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
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11
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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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12
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Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures. Forensic Sci Int Genet 2022; 59:102705. [DOI: 10.1016/j.fsigen.2022.102705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 03/10/2022] [Accepted: 04/10/2022] [Indexed: 12/13/2022]
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13
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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.
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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
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14
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Yang J, Chen J, Ji Q, Yu Y, Li K, Kong X, Xie S, Zhan W, Mao Z, Yu Y, Li D, Chen P, Chen F. A highly polymorphic panel of 40-plex microhaplotypes for the Chinese Han population and its application in estimating the number of contributors in DNA mixtures. Forensic Sci Int Genet 2021; 56:102600. [PMID: 34688115 DOI: 10.1016/j.fsigen.2021.102600] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 08/29/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022]
Abstract
Microhaplotypes (MHs) have great potential in multiple forensic applications and have proven to be promising markers in complex DNA mixture analysis. In this study, we developed a multiplex panel of 40 highly polymorphic MHs for the Chinese Han population, evaluated its forensic values, and explored its application in predicting the number of contributors (NOCs) in DNA mixtures. The panel consisted of 20 newly proposed loci and 20 previously reported loci with lengths spanning less than 120 bp. The average effective number of alleles (Ae) was 3.77, and the cumulative matching probability (CMP) and the cumulative power of exclusion (CPE) reached 1.2E-37 and 1-2.1E-12, respectively, in the Chinese Han population from the 1000 Genomes Project. Further validation on 150 Chinese Han individuals showed that Ae ranged from 2.62 to 4.41 with a mean value of 3.61, and CMP and CPE were 3.61E-36 and 1-1.84E-12, respectively, indicating that this panel was informative for personal identification and paternity testing in the studied population. To estimate NOC in DNA mixtures, we developed a machine learning model based on this panel. As a result, the accuracies in artificial DNA mixtures reached 95.24% for 2- to 4-person mixtures and 83.33% for 2- to 6-person mixtures. Furthermore, the NOC estimation on simulated profiles with allele dropout showed that this panel was still robust under slight dropout. In conclusion, this panel has value for forensic identification and NOC estimation of DNA mixtures.
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Affiliation(s)
- Jiawen Yang
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Ji Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Qiang Ji
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Youjia Yu
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Kai Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Xiaochao Kong
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Sumei Xie
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Wenxuan Zhan
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Zhengsheng Mao
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Yanfang Yu
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Ding Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Peng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
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15
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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: 13] [Impact Index Per Article: 4.3] [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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16
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Wen D, Sun S, Liu Y, Li J, Yang Z, Kureshi A, Fu Y, Li H, Jiang B, Jin C, Cai J, Zha L. Considering the flanking region variants of nonbinary SNP and phenotype-informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications. Electrophoresis 2021; 42:1115-1126. [PMID: 33483973 DOI: 10.1002/elps.202000341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 12/15/2022]
Abstract
The flanking region variants of nonbinary SNPs and phenotype-informative SNPs (piSNPs) have been observed, which may greatly improve the discriminative ability after constituting microhaplotype. In this study, 30 microhaplotype loci based on the nonbinary SNPs and piSNPs (shown to be related to phenotypes such as hair and eye color) were selected. Genotyping were conducted on 100 unrelated northern Han Chinese, and the 26 populations from the 1000 Genome Project were also included for comparison of populations differentiation. The simulated study was conducted for evaluating the efficiency of kinship testing. These 30 microhaplotype loci we selected had good polymorphism, with a mean effective number of alleles (Ae) of 3.46. The average Ae increase was 1.27 compared with the target SNPs. The populations from the five regions worldwide could also be distinguished using these loci. The results of kinship testing showed that these microhaplotype loci had the similar ability as 15 STR loci of AmpFlSTRR IdentifilerR PCR Amplification Kit to identify the biological parent and a stronger ability to exclude the nonbiological parents. So, these 30 microhaplotype loci may be multifunctional for forensic application, including the ability of personal identification and kinship testing equivalent to 15 STR loci, and the power of ancestry inference for distinguishing the main intercontinental population. Moreover, our selected phenotypic microhaplotype loci may theoretically have phenotype prediction capabilities. But the phenotype prediction efficiency of these phenotypic microhaplotype loci may be worse than that of piSNPs and the detailed prediction accuracy of different populations needs to be further studied.
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Affiliation(s)
- Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Shule Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Ying Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Zedeng Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Aliye Kureshi
- School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, P. R. China
| | - Yan Fu
- Huazhi Biotech Co., Ltd, Changsha, P. R. China
| | - Henan Li
- Microanaly Gene Technologies Co., Ltd, Hefei, P. R. China
| | - Bowei Jiang
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, P. R. China
| | - Chuan Jin
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, P. R. China
| | - Jifeng Cai
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
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17
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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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18
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Ma G, Cong B, Li S. AUCP: An indicator for system effectiveness of panels in pairwise distant kinship identification. Forensic Sci Int 2020; 316:110539. [DOI: 10.1016/j.forsciint.2020.110539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/15/2020] [Accepted: 10/05/2020] [Indexed: 11/26/2022]
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19
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Jin X, Zhang X, Shen C, Liu Y, Cui W, Chen C, Guo Y, Zhu B. A Highly Polymorphic Panel Consisting of Microhaplotypes and Compound Markers with the NGS and Its Forensic Efficiency Evaluations in Chinese Two Groups. Genes (Basel) 2020; 11:genes11091027. [PMID: 32883034 PMCID: PMC7565596 DOI: 10.3390/genes11091027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Novel genetic markers like microhaplotypes and compound markers show promising potential in forensic research. Based on previously reported single nucleotide polymorphism (SNP) and insertion/deletion (InDel) polymorphism loci, 29 genetic markers including 22 microhaplotypes and seven compound markers were identified. Genetic distributions of the 29 loci in five continental populations, Kazak and Mongolian groups in China were investigated. We found that the expected heterozygosity values of these 29 loci were >0.4 in these populations, indicating these loci were relatively high polymorphisms. Population genetic analyses of five continental populations showed that five loci displayed relatively high genetic variations among these continental populations and could be useful markers for ancestry analysis. In summary, the 29 loci displayed relatively high genetic diversities in continental populations and Chinese two groups and could be informative loci for forensic research.
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Affiliation(s)
- Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Chunmei Shen
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi’an 710062, China;
| | - Yanfang Liu
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.J.); (X.Z.); (W.C.); (C.C.); (Y.G.)
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- Correspondence: ; Tel.: +86-020-61648787
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20
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Ou X, Qu N. Noninvasive prenatal paternity testing by target sequencing microhaps. Forensic Sci Int Genet 2020; 48:102338. [PMID: 32593163 DOI: 10.1016/j.fsigen.2020.102338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/21/2020] [Accepted: 06/10/2020] [Indexed: 01/14/2023]
Abstract
Microhaplotypes (i.e.,microhaps or MHs) are emerging multi-allelic markers with at least two single nucleotide polymorphisms (SNPs) within ∼ 200 bp that have alleles of the same length and do not generate stutter products. Based on massively parallel sequencing (MPS) technology, microhaps have proven applicability in forensics for different application purposes. Here we evaluate the feasibility of non-invasive prenatal paternity testing (NIPPT) with a panel of polymorphic microhap markers, using cell-free DNA (cfDNA) in the maternal circulation. A custom MPS-based assay targeting 60 microhaps was developed in our previous study. Herein, we applied the developed assay to cfDNA samples in 15 NIPPT cases in the first trimester of pregnancy (6∼13 weeks). The R package relMix was employed for data interpretation, with a regression dropout estimating model. As a result, the targeted sequencing wherein target enrichment is by hybridization capture can be effectively employed for microhap sequencing with cfDNA samples. With the combined use of relMix, the paternity of the biological fathers in 15 cases was correctly determined, with the combined paternity index (CPI) value > 1012. Moreover, the specificity of this approach was validated by the successful paternity exclusion of 3 close relatives (father, full sibling and uncle) of the biological father in one case, and further by the significant separation in CPI distribution between the biological father and 112 unrelated males in each cases. Our results indicate that this MPS-based microhap sequencing strategy could be utilized in NIPPT. This method may contribute to developments in NIPPT and to the resolution of issues related to DNA mixtures of close relatives for specific purposes.
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Affiliation(s)
- Xueling Ou
- 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.
| | - Ning Qu
- 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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21
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Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives. Forensic Sci Int Genet 2020; 46:102255. [DOI: 10.1016/j.fsigen.2020.102255] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/12/2019] [Accepted: 01/20/2020] [Indexed: 11/22/2022]
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22
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Kureshi A, Li J, Wen D, Sun S, Yang Z, Zha L. Construction and forensic application of 20 highly polymorphic microhaplotypes. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191937. [PMID: 32537197 PMCID: PMC7277291 DOI: 10.1098/rsos.191937] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Microhaplotype markers have become an important research focus in forensic genetics. However, many reported microhaplotype markers have limited polymorphisms. In this study, we developed a set of highly polymorphic microhaplotype markers based on tri-allelic single-nucleotide polymorphisms. Eleven newly discovered microhaplotypes along with nine previously identified in our laboratory were studied. The microhaplotype genotypes of unrelated individuals and familial samples were generated on the MiSeq PE300 platform. These 20 loci have an average greater than 3.5 effective number of alleles. Over the whole set, the cumulative power of discrimination was 1-3.3 × 10-18, the cumulative power of exclusion was 1-1.928 × 10-7 and the theoretical probability of detecting a mixture was 1-1.427 × 10-6. Differentiation comparisons of 26 populations from the 1000 Genomes Project distinguished among East Asian, South Asian, African and European populations. Overall, these markers enrich the current microhaplotype marker databases and can be applied for individual identification, paternity testing and biogeographic ancestry distinction.
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Affiliation(s)
- Aliye Kureshi
- School of Basic Medical Sciences, Xinjiang Medical University, Urumqi 830011, Xinjiang, People's Republic of China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China
| | - Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China
| | - Shule Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China
| | - Zedeng Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China
| | - Lagabaiyila Zha
- School of Basic Medical Sciences, Xinjiang Medical University, Urumqi 830011, Xinjiang, People's Republic of China
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai 200063, People's Republic of China
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan, People's Republic of China
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23
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Qu N, Lin S, Gao Y, Liang H, Zhao H, Ou X. A microhap panel for kinship analysis through massively parallel sequencing technology. Electrophoresis 2019; 41:246-253. [PMID: 31816113 DOI: 10.1002/elps.201900337] [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: 09/07/2019] [Revised: 11/07/2019] [Accepted: 12/03/2019] [Indexed: 12/31/2022]
Abstract
It is widely recognized that microhaps are powerful markers for different forensic purposes, mainly due to their advantages of both short tandem repeats and single nucleotide polymorphisms, including multiple alleles, low mutation rate, and absence of stutter peaks. In the present study, a panel of 60 microhap loci was developed and utilized in forensic kinship analysis as a preliminary study. Genotyping of microhap was performed by massively parallel sequencing and haplotypes were directly achieved from sequence reads of 73 samples from Chinese Han population. We observed that 49 out of 60 loci have effective number of alleles greater than 3.0 and 10 out of 60 have values above 4.0, with an average value of 3.5598. The heterozygosity values were in a range from 0.5840 to 0.8546 with an average of 0.7268 and the cumulative power of exclusion value of the 60 loci is equal to 1-4.78 × 10-18 . Moreover, we demonstrated the applicability of this method by different relationship inference problems, including identification of single parent-offspring, full-sibling, and second-degree relative. The results indicated that the assembled microhap panel provided more power for relationship inference, than commonly used short tandem repeats or single nucleotide polymorphism system.
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Affiliation(s)
- Ning Qu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, P. R. China
| | - Shaobin Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. China
| | - Yu Gao
- Department of Obstetrics, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. China
| | - Hao Liang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hu Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, P. R. China
| | - Xueling Ou
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, P. R. China
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