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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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Tan M, Xue J, Wu Q, Zheng Y, Liu G, Zhang R, Wu M, Song J, Xiao Y, Chen D, Lv M, Liao M, Qu S, Liang W. Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing. Electrophoresis 2024; 45:463-473. [PMID: 37946554 DOI: 10.1002/elps.202300195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300 bp. Further, we successfully developed and evaluated an NGS-based panel comprising 55 loci, of which 24 were composed of both SNPs and InDels. Analysis of 124 unrelated Southern Han Chinese revealed an average effective number of alleles (Ae ) of 7.52 for this panel. The cumulative power of discrimination and cumulative probability of exclusion values of the 55 loci were 1-2.37 × 10-73 and 1-1.19 × 10-28 , respectively. Additionally, this panel exhibited high allele detection rates of over 97% in each of the 21 artificial mixtures involving from two to six contributors at different mixing ratios. We used EuroForMix to calculate the likelihood ratio (LR) and evaluate the evidence strength provided by this panel, and it could assess evidence strength with LR, distinguishing real and noncontributors. In conclusion, our panel holds great potential for detecting and analyzing DNA mixtures in forensic applications, with the capability to enhance routine mixture analysis.
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Affiliation(s)
- Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Mengna Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jinlong Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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Tomas C, Rodrigues P, Jønck CG, Barekzay Z, Simayijiang H, Pereira V, Børsting C. Performance of a 74-Microhaplotype Assay in Kinship Analyses. Genes (Basel) 2024; 15:224. [PMID: 38397213 PMCID: PMC10888013 DOI: 10.3390/genes15020224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory.
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Affiliation(s)
| | | | | | | | | | | | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V’s Vej 11, DK-2100 Copenhagen, Denmark; (C.T.); (P.R.); (C.G.J.); (Z.B.); (V.P.)
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Wang H, Kang B, Gao Y, Zhang M, Jiang J, Su J, Zhang B, Zhu B, Liao S. Construction and evaluation of a novel set of 90 microhaplotypes for forensic applications using NGS technology. Forensic Sci Int 2023; 353:111848. [PMID: 37890263 DOI: 10.1016/j.forsciint.2023.111848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/27/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023]
Abstract
Microhaplotypes (MHs), small sets of linked single nucleotide polymorphisms (SNPs), are becoming a valuable tool for paternity testing, personal identification and other different forensic purposes due to their advantages of both short tandem repeats (STRs) and SNPs. However, only a small part of MHs with small segments have been developed and reported so far. And the current population genetic data of MHs are still insufficient. MHs with small segments possess unique advantages in mixture deconvolution, degradation material identification, noninvasive prenatal paternity testing and even medical tumor diagnostic applications. In the present study, a set of 90 autosomal MHs whose PCR amplicon lengths are from 90-150 bp, of which 58 MHs are less than or equal to 100 bp are selected, and assembled into an amplification multiplex system optimized for Ion S5™ System for forensic application. Genetic diversity study of 90 MHs in the populations from different intercontinental regions shows that the polymorphism information content (PIC) values of 83 MHs are greater than 0.4 in populations from East Asia (EAS), and the average PIC value of 90 MHs is greater than 0.5. A total of EAS populations shows the highest cumulative match probability (CMP) and cumulative probability of exclusion (CPE) values in five intercontinental populations. The CMP and CPE values of 90 MHs in EAS are 1.1688 × 10-54 and 0.999999999998954. The informativeness for assignment (In) values of the 90 MHs are calculated based on data from five intercontinental populations, and the In values of 20 MHs have greater than 0.1, indicating that the 20 MHs are high effectiveness in distinguishing different intercontinental populations, which can be used as candidate ancestry informative markers. Further, we have studied the polymorphisms of the 90 MHs based on 224 unrelated individuals of Henan Han population, China, and obtained the frequency data of the 90 MHs. In the Henan Han population, the effective number of alleles (Ae) of the 90 MHs ranges from 1.7649 (MH45) to 3.9792 (MH50), and the Ae values of 10 MHs reach to 3.0; the Ae values of 80 MHs are greater than 2, and the average Ae value for these MHs is 2.422. The average expected heterozygosity, observed heterozygosity, PIC, matching probability, discrimination power and probability of exclusion values of 90 MHs in the Henan Han population are 0.5788, 0.5851, 0.5039, 0.2608, 0.7392 and 0.2806, respectively. The CMP value of 90 MHs in the study population is less than 10-54, and their CPE value reaches 0.999999999999999923. Moreover, the results of the depth of coverage, allele coverage ratio and noise level indicate that the 90 MH amplification system has well sequencing performance, and the sequencing results are reliable. The results indicate the 90 MHs show higher polymorphisms in the study population. The present panel can be well used in paternity testing and individual identification in the study population and even the populations from EAS.
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Affiliation(s)
- Hongdan Wang
- College of Forensic Science, Xi'an Jiaotong University Health Science Center, Xi'an, China; Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China; National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Bing Kang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Yue Gao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Mengting Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Jincheng Jiang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Junxiang Su
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Bo Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Bofeng Zhu
- College of Forensic Science, Xi'an Jiaotong University Health Science Center, Xi'an, China; Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China.
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Wen Y, Liu J, Su Y, Chen X, Hou Y, Liao L, Wang Z. Forensic biogeographical ancestry inference: recent insights and current trends. Genes Genomics 2023; 45:1229-1238. [PMID: 37081293 DOI: 10.1007/s13258-023-01387-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/01/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND As a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in human forensic investigation especially when a database hit or eyewitness testimony are not available. It indicates one's biogeographical profile based on known population-specific genetic variations, and thus is crucial for guiding authority investigations to find unknown individuals. Forensic biogeographical ancestry testing exploits much of the recent advances in the understanding of human genomic variation and improving of molecular biology. OBJECTIVE In this review, recent development of prospective ancestry informative markers (AIMs) and the statistical approaches of inferring biogeographic ancestry from AIMs are elucidated and discussed. METHODS We highlight the research progress of three potential AIMs (i.e., single nucleotide polymorphisms, microhaplotypes, and Y or mtDNA uniparental markers) and discuss the prospects and challenges of two methods that are commonly used in BGAI. CONCLUSION While BGAI for forensic purposes has been thriving in recent years, important challenges, such as ethics and responsibilities, data completeness, and ununified standards for evaluation, remain for the use of biogeographical ancestry information in human forensic investigations. To address these issues and fully realize the value of BGAI in forensic investigation, efforts should be made not only by labs/institutions around the world independently, but also by inter-lab/institution collaborations.
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Affiliation(s)
- Yufeng Wen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu, 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Linchuan Liao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Zheng Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China.
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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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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9
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Kwon YL, Lee EY, Kim BM, Joo SM, Jeong KS, Chun BW, Lee YH, Park KW, Shin KJ. Application of a custom haplotype caller to analyze sequence-based data of 56 microhaplotypes. Forensic Sci Int Genet 2022; 61:102778. [PMID: 36166997 DOI: 10.1016/j.fsigen.2022.102778] [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: 03/30/2022] [Revised: 08/23/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022]
Abstract
Microhaplotypes (microhaps) are recently introduced markers that aim to complement the limitations of conventional forensic markers such as short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). With the potential of microhaps in forensics becoming clearer through massively parallel sequencing (MPS), MPS-based studies on microhaps are being actively reported. However, simpler workflow schemes for the generation and analysis of MPS data are still required to facilitate the practical application of MPS in forensics. In this study, we developed an in-house MPS panel that simultaneously amplifies 56 microhaps and a custom haplotype caller, Visual Microhap. The developed tool works on a web browser and provides four analysis options to extract SNP-based haplotypes from sequence-based data obtained by STRait Razor 3.0. To demonstrate the utility of the MPS panel and data analysis workflow scheme, we also analyzed 56 microhaps of 286 samples from four populations (African-American, Caucasian, Hispanic, and Korean). The average effective number of alleles (Ae) for the four groups was 3.45, ranging from 1.74 to 6.98. Forensic statistical parameters showed that this microhap panel is more powerful than conventional autosomal STRs for human identification. Meanwhile, the 56-plex panel mostly comprised microhaps with high Ae; however, the four populations were grossly distinguishable from each other by cluster analysis. Consequently, the developed in-house MPS panel for 56 microhaps and the adopted workflow using open-source tools can increase the utility of microhap MPS in forensic research and practice.
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Affiliation(s)
- Ye-Lim Kwon
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, Seoul 03722, Republic of Korea.
| | - Eun Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea. -silver02-@hanmail.net
| | - Bo Min Kim
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, Seoul 03722, Republic of Korea.
| | - Su Min Joo
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, Seoul 03722, Republic of Korea.
| | - Kyu Sik Jeong
- Forensic DNA division, National Forensic Service, Wonju-si, Gangwon-do 26460, Republic of Korea.
| | - Byung Won Chun
- DNA analysis Division, National Forensic Service Daejeon Institute, Daejeon 34054, Republic of Korea.
| | - Yang Han Lee
- Forensic DNA division, National Forensic Service, Wonju-si, Gangwon-do 26460, Republic of Korea.
| | - Ki Won Park
- Forensic DNA division, National Forensic Service, Wonju-si, Gangwon-do 26460, Republic of Korea.
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, Seoul 03722, Republic of Korea.
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10
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Kidd KK, Pakstis AJ, Gandotra N, Scharfe C, Podini D. A multipurpose panel of microhaplotypes for use with STR markers in casework. Forensic Sci Int Genet 2022; 60:102729. [PMID: 35696960 PMCID: PMC11071123 DOI: 10.1016/j.fsigen.2022.102729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/19/2022]
Abstract
A small panel of highly informative loci that can be genotyped on the same equipment as the standard CODIS short tandem repeat (STR) markers has strong potential for application in forensic casework. Single nucleotide polymorphisms (SNPs) can be typed by a couple of methods on capillary electrophoresis (CE) machines and on sequencers, but the amount of information relative to the laboratory effort has hindered use of SNPs in actual casework. Insertion-deletion markers (InDels) suffer from similar problems. Microhaplotypes (MHs) are much more informative per locus but have similar technical difficulties unless they are typed by massively parallel sequencing (MPS). As forensic labs are acquiring sequencing machines, MHs become more likely to be used in casework, especially if multiplexed with STRs. Here we present the details of a multipurpose panel of 24 MHs with the highest effective number of alleles (Ae) from previous work. An augmented STR panel of 24 loci (20 CODIS markers plus four commonly typed STRs) is also considered. The Ae and ancestry informativeness (In) distributions of these two datasets are compared. The MH panel is shown to have better individualization and population distinction than the augmented CODIS STRs. We note that the 24 MHs should be better for mixture analyses than the STRs. Finally, we suggest that a commercial kit including both the standard CODIS markers and this set of 24 MH would greatly improve the discrimination power over that of current commercial assays.
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Affiliation(s)
- Kenneth K Kidd
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States.
| | - Andrew J Pakstis
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Neeru Gandotra
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Curt Scharfe
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Daniele Podini
- The George Washington University, Department of Forensic Science, 2100 Foxhall Road, NW, Washington, DC 20007, United States
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11
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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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12
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An overview of SNP-SNP microhaplotypes in the 26 populations of the 1000 Genomes Project. Int J Legal Med 2022; 136:1211-1226. [DOI: 10.1007/s00414-022-02820-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/25/2022] [Indexed: 10/18/2022]
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13
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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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14
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Wang Z, Qin L, Liu J, Jiang L, Zou X, Chen X, Song F, Dai H, Hou Y. Forensic nanopore sequencing of microhaplotype markers using QitanTech's QNome. Forensic Sci Int Genet 2021; 57:102657. [PMID: 34973558 DOI: 10.1016/j.fsigen.2021.102657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/20/2022]
Abstract
In recent years, extraordinary progress has been made in genome sequencing technologies, which has led to a decrease in cost and an increase in the diversity of sequenced genomes. Nanopore sequencing is one of the latest genome sequencing technologies. It aims to sequence longer contiguous pieces of DNA, which are essential for resolving structurally complex regions, and provides a new approach for forensic genetics to detect longer markers in real time. To date, multiple studies have been conducted to sequence forensic markers using MinION from Oxford Nanopore Technologies (ONT), and the results indicate that nanopore sequencing holds promise for forensic applications. Qitan Technology (QitanTech) recently launched its first commercial nanopore genome sequencer, QNome. It could achieve a read length of more than 150 kbp, and could generate approximately 500 Mb of data in 8 h. In this pilot study, we explored and validated this alternative nanopore sequencing device for microhaplotype (MH) profiling using a custom set of 15 MH loci. Seventy single-contributor samples were divided into 7 batches, each of which included 10 samples and control DNA 9947A and was sequenced by QNome. MH genotypes generated from QNome were compared to those from Ion Torrent sequencing (Ion S5XL system) to evaluate the accuracy and stability. Twelve samples randomly selected from the last three batches and Control DNA 9947A were also subjected to ONT MinION sequencing (with R9.4 flow cell) for parallel comparison. Based on MHtyper, a bioinformatics workflow developed for automated MH designation, all MH loci can be genotyped and reliably phased using the QNome data, with an overall accuracy of 99.83% (4 errors among 2310 genotypes). Three occurred near or in the region of homopolymer sequences, and one existed within 50 bp of the start of the sequencing reaction. In the last 15 samples (12 individual samples and 3 replicates of control DNA 9947A), two SNPs located at 4-mer homopolymers failed to obtain reliable genotypes on the MinION data. This study shows the potential of state-of-the-art nanopore sequencing methods to analyze forensic MH markers. Given the rapid pace of change, sporadic and nonrepetitive errors presented in this study are expected to be resolved by further developments of nanopore technologies and analysis tools.
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Affiliation(s)
- Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Liu Qin
- Qitan Technology Ltd., Chengdu 610044, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiameng Chen
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hao Dai
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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15
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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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16
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Pakstis AJ, Gandotra N, Speed WC, Murtha M, Scharfe C, Kidd KK. The population genetics characteristics of a 90 locus panel of microhaplotypes. Hum Genet 2021; 140:1753-1773. [PMID: 34643790 PMCID: PMC8553733 DOI: 10.1007/s00439-021-02382-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and small genomic regions with multiple SNPs (microhaplotypes, MHs) are rapidly emerging as novel forensic investigative tools to assist in individual identification, kinship analyses, ancestry inference, and deconvolution of DNA mixtures. Here, we analyzed information for 90 microhaplotype loci in 4009 individuals from 79 world populations in 6 major biogeographic regions. The study included multiplex microhaplotype sequencing (mMHseq) data analyzed for 524 individuals from 16 populations and genotype data for 3485 individuals from 63 populations curated from public repositories. Analyses of the 79 populations revealed excellent characteristics for this 90-plex MH panel for various forensic applications achieving an overall average effective number of allele values (Ae) of 4.55 (range 1.04–19.27) for individualization and mixture deconvolution. Population-specific random match probabilities ranged from a low of 10–115 to a maximum of 10–66. Mean informativeness (In) for ancestry inference was 0.355 (range 0.117–0.883). 65 novel SNPs were detected in 39 of the MHs using mMHseq. Of the 3018 different microhaplotype alleles identified, 1337 occurred at frequencies > 5% in at least one of the populations studied. The 90-plex MH panel enables effective differentiation of population groupings for major biogeographic regions as well as delineation of distinct subgroupings within regions. Open-source, web-based software is available to support validation of this technology for forensic case work analysis and to tailor MH analysis for specific geographical regions.
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Affiliation(s)
- Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Michael Murtha
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA.
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17
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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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18
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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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19
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Genetic relationships of Southwest Asian and Mediterranean populations. Forensic Sci Int Genet 2021; 53:102528. [PMID: 34020230 DOI: 10.1016/j.fsigen.2021.102528] [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: 01/04/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 11/23/2022]
Abstract
The Southwest Asian, circum-Mediterranean, and Southern European populations (collectively, SWAMSE) together with Northern European populations form one of five "continental" groups of global populations in many analyses of population relationships. This region is of great anthropologic and forensic interest but relationships of large numbers of populations within the region have not been able to be cleanly resolved with autosomal genetic markers. To examine the genetic boundaries to the SWAMSE region and whether internal structure can be detected we have assembled data for a total of 151 separate autosomal genetic markers on populations in this region and other parts of the world for a global set of 95 populations. The markers include 83 ancestry informative SNPs as singletons and 68 microhaplotype loci defined by 204 SNPs. The 151 loci are ancestry informative on a global scale, identifying at least five biogeographic clusters. One of those clusters is a clear grouping of 37 populations containing the SWAMSE plus northern European populations to the exclusion of populations in South Central Asia and populations from farther East. A refined analysis of the 37 populations shows the northern European populations clustering separately from the SWAMSE populations. Within Southwest Asia the Samaritans and Shabaks are distinct outliers. The Yemenite Jews, Saudi, Kuwaiti, Palestinian Arabs, and Southern Tunisians cluster together loosely while the remaining populations from Northern Iraq, Mediterranean Europe, the Caucasus region, and Iran cluster in a more complex graded fashion. The majority of the SWAMSE populations from the mainland of Southwest Asia form a cluster with little internal structure reflecting a very complex history of endogamy and migrations. The set of 151 DNA polymorphisms not only distinguishes major geographical regions globally but can distinguish ancestry to a small degree within geographical regions such as SWAMSE. We discuss forensic characteristics of the polymorphisms and also identify those that rank highest by Rosenberg's In measure for the SWAMSE region populations and for the global set of populations analyzed. DATA AVAILABILITY: Genotypes on all 151 markers for all 3790 individuals typed in the Kidd Lab on the 72 Kidd lab populations have been deposited in the Zenodo archive and can be freely accessed at https://doi.org/10.5281/zenodo.4658892. Some of the data has been made public previously as supplemental files appended to publications. Data for the additional individuals included in the analyses was taken from already public datasets as indicated in the text.
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20
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Wu R, Li H, Li R, Peng D, Wang N, Shen X, Sun H. Identification and sequencing of 59 highly polymorphic microhaplotypes for analysis of DNA mixtures. Int J Legal Med 2021; 135:1137-1149. [PMID: 33502549 DOI: 10.1007/s00414-020-02483-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/09/2020] [Indexed: 12/30/2022]
Abstract
Mixture detection remains one of the major challenges within a forensic science context. In recent years, microhaplotypes were proposed to have great potential in mixture detection, although many of them are not as polymorphic as widely used short tandem repeat (STR) markers. In this study, 59 new highly polymorphic microhaplotypes were identified and sequenced with the NextSeq 500 Sequencer. Based on the whole 1000 Genomes Project dataset, the average effective number of alleles (Ae) of the 59 microhaplotypes was 5.44, and the Ae values of 36 of these microhaplotypes were > 5.00. Their genetic variations in 187 Han Chinese individuals were evaluated. The average allele coverage ratio (ACR) of heterozygotes across all loci was 0.96 ± 0.05. The number of observed alleles varied from 4 to 23, with an average of 8.8 alleles per microhaplotype locus. The average observed heterozygosity (Ho) of 59 loci was 0.77 ± 0.05, and the Ho values of 15 of these loci were > 0.80. All loci showed high polymorphisms with a discrimination power (DP) ranging from 0.80 to 0.97, and the average DP was 0.92 ± 0.03. The analysis of simulated mixtures demonstrated that the microhaplotypes reported here were highly polymorphic and performed well in forensic DNA mixture analysis. This study not only demonstrated the applicability of microhaplotypes in mixture analysis but also provided new choices for highly polymorphic microhaplotypes because after adding the markers identified here, the number of microhaplotypes with Ae values of > 4.00 will increase from ~ 50 to ~ 110.
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Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.
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21
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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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22
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Oldoni F, Bader D, Fantinato C, Wootton SC, Lagacé R, Kidd KK, Podini D. A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures. Forensic Sci Int Genet 2020; 49:102367. [DOI: 10.1016/j.fsigen.2020.102367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
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23
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Qu S, Lv M, Xue J, Zhu J, Wang L, Jian H, Liu Y, Zhang R, Zha L, Liang W, Zhang L. Multi-Indel: A Microhaplotype Marker Can Be Typed Using Capillary Electrophoresis Platforms. Front Genet 2020; 11:567082. [PMID: 33193656 PMCID: PMC7649793 DOI: 10.3389/fgene.2020.567082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022] Open
Abstract
Since the concept of microhaplotypes was proposed by Kidd in 2013, various microhaplotype markers have been investigated for various forensic purposes, such as individual identification, deconvolution of DNA mixtures, or forensic ancestry inference. In our opinion, various compound markers are also regarded as generalized microhaplotypes, encompassing two or more variants in a short segment of DNA (e.g., 200 bp). That is, a set of variants (referred to herein as multi-variants) within a certain length includes single nucleotide polymorphisms (SNP), insertion/deletion polymorphisms (Indels), or short tandem repeat polymorphisms (STRs). At present, multi-variant is mainly aimed at multi-SNPs. However, the haplotype genotyping of multi-variants relies on single-strand analysis, mainly using massively parallel sequencing (MPS). Here, we describe a method based on a capillary electrophoresis (CE) platform that can directly obtain haplotypes of individuals. Several microhaplotypes consisting of three or more Indels with different insertion or deletion lengths in the range of less than 200 bp were screened out, each of which had at least three haplotypes. As a result, the haplotype of an individual was reflected by the length of its polymorphism. Finally, we established a multiplex amplification system containing 18 multi-Indel markers that could identify haplotypes on each chromosome of an individual. The combined power of discrimination (CPD) and the cumulative probability of exclusion (CPE) were 0.999999999997234 and 0.9984, respectively.
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Affiliation(s)
- Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jing Zhu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.,Department of Forensic Medicine, Sichuan Police College, Luzhou, 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 (Sichuan University), Ministry of Education, Chengdu, China
| | - Hui Jian
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuqing Liu
- 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
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
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24
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de la Puente M, Ruiz-Ramírez J, Ambroa-Conde A, Xavier C, Amigo J, Casares de Cal MÁ, Gómez-Tato A, Carracedo Á, Parson W, Phillips C, Lareu MV. Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data. Front Genet 2020; 11:581041. [PMID: 33193704 PMCID: PMC7606911 DOI: 10.3389/fgene.2020.581041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/25/2020] [Indexed: 11/13/2022] Open
Abstract
The development of microhaplotype (MH) panels for massively parallel sequencing (MPS) platforms is gaining increasing relevance for forensic analysis. Here, we expand the applicability of a 102 autosomal and 11 X-chromosome panel of MHs, previously validated with both MiSeq and Ion S5 MPS platforms and designed for identification purposes. We have broadened reference population data for identification purposes, including data from 240 HGDP-CEPH individuals of native populations from North Africa, the Middle East, Oceania and America. Using the enhanced population data, the panel was evaluated as a marker set for bio-geographical ancestry (BGA) inference, providing a clear differentiation of the five main continental groups of Africa, Europe, East Asia, Native America, and Oceania. An informative degree of differentiation was also achieved for the population variation encompassing North Africa, Middle East, Europe, South Asia, and East Asia. In addition, we explored the potential for individual BGA inference from simple mixed DNA, by simulation of mixed profiles followed by deconvolution of mixture components.
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Affiliation(s)
- María de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.,Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Jorge Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Adrián Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Jorge Amigo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | | | - Antonio Gómez-Tato
- Faculty of Mathematics, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, PA, United States
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - María Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
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25
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Population genetic data of 74 microhaplotypes in four major U.S. population groups. Forensic Sci Int Genet 2020; 49:102398. [PMID: 33045522 DOI: 10.1016/j.fsigen.2020.102398] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/10/2020] [Accepted: 09/19/2020] [Indexed: 12/30/2022]
Abstract
Microhaplotypes (microhaps or MHs) are novel forensically relevant genetic markers that demand large and appropriate allele frequency datasets for their implementation in casework. In this study we report on the allele frequency data of 74 microhap loci (230 SNPs) included in a newly developed 74-plex assay. The panel was tested on the Ion S5 system on a total of 347 samples from four main U.S. population groups of African, European, East Asian and Southwest Hispanic descent. Overall, frequencies of individual alleles at each locus varied considerably among the different population groups. An increase in the average value of gene diversity was also observed as the number of SNPs per locus increased. Most microhap markers showed no significant deviation from Hardy-Weinberg ratios within any of the individual population samples displaying an average power of discrimination between 0.74 and 0.81 and an average probability of exclusion between 0.32 and 0.39. Moreover, the four population groups had no clear genetic affinities with the exception of U.S. European and U.S. Southwest Hispanic populations, which showed the lowest FST value. STRUCTURE and principal component analyses (PCA) analysis resulted in effective clustering of the four populations with the U.S. European and Southwest Hispanic showing some overlap. These results support the potential use of this sequence-based 74plex-microhaplotype assay for ancestry inference in addition to previously reported human identification and mixture deconvolution capabilities.
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26
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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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27
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Validation of novel forensic DNA markers using multiplex microhaplotype sequencing. Forensic Sci Int Genet 2020; 47:102275. [PMID: 32305739 PMCID: PMC10131188 DOI: 10.1016/j.fsigen.2020.102275] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/22/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022]
Abstract
Microhaplotypes (MH) are comprised of multiple single nucleotide polymorphisms (SNPs) that are located within 300 bases of genomic sequence. Improved tools are needed to facilitate broader application of microhaplotypes in a diverse range of populations and forensic settings. We designed an assay for multiplex sequencing of 90 microhaplotypes (mMHseq) that include 46 MH loci with high Effective Number of Alleles (Ae) from previous studies [1], and 44 high Ae MH loci containing between four to fourteen SNPs that were identified from the 1000 Genomes (1KG) Project. The unique design of mMHseq integrates a novel method for multiplex amplification from small DNA amounts, and multiplex sequencing of 48 samples in a single MiSeq run to detect all relevant MH variation. Assay performance was evaluated in a cohort of 156 individuals from seven different world populations from Africa, Asia, and Europe. Three of those populations from East Africa (Chagga, Sandawe, and Zaramo) and one from Eastern Europe (Adygei) had sufficient individuals sequenced by the assay to be included in statistical analyses with the 26 1KG populations. For those 30 populations the mean global average Ae was 5.08 (range: 2.7-11.54) and mean informativeness for biogeographic variation (In) was 0.30 (range: 0.08-0.70). Eighty-five novel SNPs were detected in 58 of the 90 microhaplotypes. Open-source, web-based software was developed to visualize haplotype phase data for each microhaplotype and individual. Our approach for multiplex microhaplotype sequencing can be customized and expanded as novel loci are being discovered.
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28
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Jin X, Cui W, Chen C, Guo Y, Zhang X, Xing G, Lan J, Zhu B. Developing and population analysis of a new multiplex panel of 18 microhaplotypes and compound markers using next generation sequencing and its application in the Shaanxi Han population. Electrophoresis 2020; 41:1230-1237. [DOI: 10.1002/elps.201900451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/03/2020] [Accepted: 04/17/2020] [Indexed: 01/05/2023]
Affiliation(s)
- Xiao‐Ye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
- College of Forensic Science Xi'an Jiaotong University Health Science Center Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
- College of Forensic Science Xi'an Jiaotong University Health Science Center Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
- College of Forensic Science Xi'an Jiaotong University Health Science Center Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
| | - Yu‐Xin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
- College of Forensic Science Xi'an Jiaotong University Health Science Center Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
| | - Xing‐Ru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
- College of Forensic Science Xi'an Jiaotong University Health Science Center Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
| | - Guo‐Hui Xing
- People's Hospital of Arong Banner Hulunbuir P. R. China
| | - Jiang‐Wei Lan
- Multi‐Omics Innovative Research Center of Forensic Identification Department of Forensic Genetics, School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Bo‐Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology Xi'an Jiaotong University Xi'an P. R. China
- Multi‐Omics Innovative Research Center of Forensic Identification Department of Forensic Genetics, School of Forensic Medicine Southern Medical University Guangzhou P. R. China
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29
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Liu J, Hao T, Cheng X, Wang J, Li W, Liu Z, Shi J, Li Z, Ren J, Yun K, Zhang G. DIP-microhaplotypes: new markers for detection of unbalanced DNA mixtures. Int J Legal Med 2020; 135:13-21. [PMID: 32372232 DOI: 10.1007/s00414-020-02288-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022]
Abstract
The identification of a suspect in a degraded and unbalanced DNA mixture has been a challenge for the standard short tandem repeat polymorphisms (STR) typing. Several methods have been introduced to solve this problem, such as DIP-STR, DIP-SNP, and SNP-STR markers. In this study, we proposed DIP-microhaplotype (deletion/insertion linked a chain of SNPs) as a kind of new genetic marker to type the unbalanced and degraded DNA mixture. We established the detection method with ten DIP-microhaplotype markers including 26 SNPs using allele-specific multiplex PCR followed by SNaPshot assay. This novel compound marker allows us to detect the minor DNA with a sensitivity of 1:100 to 1:1000 in a DNA mixture of any gender. Most of the DIP-microhaplotype markers had a relatively high probability of informative alleles with an average informative value (I value) of 0.308. In all, we proposed DIP-microhaplotype as a novel type of DNA marker for the detection of minor contributor from unbalanced DNA mixtures. Due to their inherent shorter length, higher polymorphism, and sensitivity, DIP-microhaplotypes are promising markers for the examination of the degraded and unbalanced mixtures in forensic stains or clinical chimeras.
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Affiliation(s)
- Jinding Liu
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Ting Hao
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Xiaojuan Cheng
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Jiaqi Wang
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Wenyan Li
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Zidong Liu
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Jie Shi
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Zeqin Li
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Jianbo Ren
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China
| | - Keming Yun
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China.
| | - Gengqian Zhang
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Wenhua Street 55#, Jinzhong, 030619, Shanxi, People's Republic of China.
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30
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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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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: 30] [Impact Index Per Article: 7.5] [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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32
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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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33
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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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34
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Turchi C, Melchionda F, Pesaresi M, Fattorini P, Tagliabracci A. Performance of a massive parallel sequencing microhaplotypes assay on degraded DNA. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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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: 44] [Impact Index Per Article: 8.8] [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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36
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Kuffel A, Gray A, Nic Daeid N. Human Leukocyte Antigen alleles as an aid to STR in complex forensic DNA samples. Sci Justice 2019; 60:1-8. [PMID: 31924284 DOI: 10.1016/j.scijus.2019.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 09/09/2019] [Accepted: 09/15/2019] [Indexed: 10/25/2022]
Abstract
Human biological samples with multiple contributors remain one of the most challenging aspects of DNA typing within a forensic science context. With the increasing sensitivity of commercially available kits allowing detection of low template DNA, complex mixtures are now a standard component of forensic DNA evidence. Over the years, various methods and techniques have been developed to try to resolve the issue of mixed profiles. However, forensic DNA analysis has relied on the same markers to generate DNA profiles for the past 30 years causing considerable challenges in the deconvolution of complex mixed samples. The future of resolving complicated DNA mixtures may rely on utilising markers that have been previously applied to gene typing of non-forensic relevance. With Massively Parallel Sequencing (MPS), techniques becoming more popular and accessible even epigenetic markers have become a source of interest for forensic scientists. The aim of this review is to consider the potential of alleles from the Human Leukocyte Antigen (HLA) complex as effective forensic markers. While Massively Parallel Sequencing of HLA is routinely used in clinical laboratories in fields such as transplantation, pharmacology or population studies, there have not been any studies testing its suitability for forensic casework samples.
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Affiliation(s)
- Agnieszka Kuffel
- Leverhulme Research Centre for Forensic Science, Ewing Building, University of Dundee, Small's Lane, Dundee DD1 4HR, United Kingdom.
| | - Alexander Gray
- Leverhulme Research Centre for Forensic Science, Ewing Building, University of Dundee, Small's Lane, Dundee DD1 4HR, United Kingdom.
| | - Niamh Nic Daeid
- Leverhulme Research Centre for Forensic Science, Ewing Building, University of Dundee, Small's Lane, Dundee DD1 4HR, United Kingdom.
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