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Liu J, Li S, Su Y, Wen Y, Qin L, Zhao M, Hui M, Jiang L, Chen X, Hou Y, Wang Z. A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing. Forensic Sci Int Genet 2024; 68:102947. [PMID: 37862770 DOI: 10.1016/j.fsigen.2023.102947] [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: 06/14/2023] [Revised: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- 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
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Liu Qin
- Qitan Technology Ltd., Chengdu 610044, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Minxiao Hui
- 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
| | - 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
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, 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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Liu J, Su Y, Wen Y, Jiang L, Li S, Zhao M, Chen X, Wang Z. Massively parallel sequencing of 74 microhaplotypes and forensic characteristics in three Chinese Sino-Tibetan populations. Forensic Sci Int Genet 2023; 66:102905. [PMID: 37301091 DOI: 10.1016/j.fsigen.2023.102905] [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: 03/11/2023] [Revised: 04/27/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
Microhaplotype (MH), as an emerging type of forensic genetic marker in recent years, has the potential to support multiple forensic applications, especially for mixture deconvolution and biogeographic ancestry inference. Herein, we investigated the genotype data of 74 MHs included in a novel MH panel, the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel, in three Chinese Sino-Tibetan populations (Han, Tibetan, and Yi) using the Ion Torrent semiconductor sequencing. The sequencing performance, allele frequencies, effective number of alleles (Ae), informativeness (In), and forensic parameters were subsequently estimated and calculated. In addition, principal component analysis (PCA) and structure analysis were performed to explore the population relationships among the three populations and the ancestry component distribution. Overall, this novel MH panel is robust and reliable, and has an excellent sequencing performance. The Ae values ranged from 1.0126 to 7.0855 across all samples, and 75.68 % of MHs had Ae values >2.0000. Allele frequencies at some loci varied considerably among the three studied populations, and the mean In value was 0.0195. Moreover, the genetic affinity between Tibetans and Yis was closer than that between Tibetans and Hans. The aforementioned results suggest that the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel is highly polymorphic in three investigated populations and could be used as an effective tool for human forensics. Although these 74 MHs have demonstrated the competency in continental population stratification, a higher resolution for distinguishing intracontinental subpopulations and a more comprehensive database with sufficient reference population data still remain to be accomplished.
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Affiliation(s)
- 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 610044, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, 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
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Mei S, Yi S, Cai M, Zhang Y, Cui W, Xu H, Lan Q, Zhu B. Exploring the forensic effectiveness and population genetic differentiation by self-constructed 41 multi-InDel panel in Yunnan Zhuang group. Gene 2023; 860:147180. [PMID: 36669579 DOI: 10.1016/j.gene.2023.147180] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Yunnan is one of the main residences of the Zhuang group which is one of the 55 ethnic minorities in China. At present, there are relatively few researches on population genetics and forensic science of the Yunnan Zhuang group. Therefore, this study used a self-constructed panel containing 41 multi-InDel markers to analyze the genetic polymorphisms of 173 individuals from Yunnan Zhuang group. The results indicated that these 41 multi-InDels in Yunnan Zhuang group were highly polymorphic markers expect for three markers. The cumulative match probability and combined exclusion probability values of the 40 multi-InDels (MI38 marker was excluded) were 8.0671E-26 and 0.9999995959, respectively. In addition, population genetic analyses were performed on genotyping data of 41 multi-InDel markers among the Yunnan Zhuang and 26 reference populations, revealing that the Yunnan Zhuang group was genetically close to the five populations in East Asia. According to the STRUCTURE analysis, the Yunnan Zhuang group presented similar ancestral compositions to the five populations from East Asia, and when the K value was three, the five intercontinental populations showed their different genetic structures. In conclusion, the 41 multi-InDel markers could be used as an effective tool for individual identification and paternity testing of the Zhuang group in Yunnan province, as well as for their ancestry information inference studies.
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Affiliation(s)
- Shuyan Mei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China
| | - Yunying Zhang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China.
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Kayser M, Branicki W, Parson W, Phillips C. Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age. Forensic Sci Int Genet 2023; 65:102870. [PMID: 37084623 DOI: 10.1016/j.fsigen.2023.102870] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland,; Institute of Forensic Research, Kraków, Poland
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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Huang S, Sheng M, Li Z, Li K, Chen J, Wu J, Wang K, Shi C, Ding H, Zhou H, Ma L, Yang J, Pu Y, Yu Y, Chen F, Chen P. Inferring bio-geographical ancestry with 35 microhaplotypes. Forensic Sci Int 2022; 341:111509. [DOI: 10.1016/j.forsciint.2022.111509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 10/04/2022] [Accepted: 10/30/2022] [Indexed: 11/24/2022]
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7
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Sun K, Yao Y, Yun L, Zhang C, Xie J, Qian X, Tang Q, Sun L. Application of machine learning for ancestry inference using multi-InDel markers. Forensic Sci Int Genet 2022; 59:102702. [DOI: 10.1016/j.fsigen.2022.102702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 01/04/2023]
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Cao Y, Zhu Q, Huang Y, Li X, Wei Y, Wang H, Zhang J. An efficient ancestry informative SNPs panel for further discriminating East Asian populations. Electrophoresis 2022; 43:1774-1783. [PMID: 35749689 DOI: 10.1002/elps.202100349] [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: 11/02/2021] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/07/2022]
Abstract
In forensic genetics, the use of ancestry informative single-nucleotide polymorphisms (AISNPs) panels can narrow the direction of the investigation by estimating an individual's biogeographic ancestry. However, distinguishing subgroups within continental regions requires more specific panels. In this study, we screened 19 AISNPs from the 1000 Genomes Project (1KG) based on their FST values to distinguish target populations in East Asia and obtained genotypes through SNaPshot. The 19 AISNPs could divide the global population of the 1KG into five clusters and could further divide the East Asian population into four clusters: Japanese, Han Chinese, Dai Chinese, and Kinh in Ho Chi Minh City of Vietnam. In summary, the 19-AISNP panel may serve as a useful and cost-effective tool for forensic ancestry inference in East Asian populations at a finer scale.
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Affiliation(s)
- Yueyan Cao
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Qiang Zhu
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yuguo Huang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Xi Li
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yifan Wei
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Haoyu Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Ji Zhang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
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Zou X, He G, Liu J, Jiang L, Wang M, Chen P, Hou Y, Wang Z. Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese subpopulations. Forensic Sci Int Genet 2022; 58:102687. [DOI: 10.1016/j.fsigen.2022.102687] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/20/2022] [Accepted: 03/11/2022] [Indexed: 11/04/2022]
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10
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Identification of missing persons through kinship analysis by microhaplotype sequencing of single-source DNA and two-person DNA mixtures. Forensic Sci Int Genet 2022; 58:102689. [DOI: 10.1016/j.fsigen.2022.102689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/22/2022] [Accepted: 03/14/2022] [Indexed: 11/04/2022]
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11
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Screening of highly discriminative microhaplotype markers for individual identification and mixture deconvolution in East Asian populations. Forensic Sci Int Genet 2022; 59:102720. [DOI: 10.1016/j.fsigen.2022.102720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/23/2022]
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12
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Could routine forensic STR genotyping data leak personal phenotypic information? Forensic Sci Int 2022; 335:111311. [PMID: 35468577 DOI: 10.1016/j.forsciint.2022.111311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/19/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022]
Abstract
The application of forensic genetic markers must comply with privacy rights and legal policies on a premise that the markers do not expose phenotypic information. The most widely-used short tandem repeats (STRs) are generally viewed as 'junk' DNA because most STRs are located in non-coding regions and therefore refrain from leaking phenotypic traits. But with a deepening understanding of phenotypes and underlying genetic structure, whether STRs could potentially reflect any phenotypic information may need re-examining. Therefore, we performed the following analyses. First, we analyzed the association between 15 STRs and three facial characteristics (single or double eyelid, with or without epicanthus, unattached or attached earlobe) on 721 unrelated Han Chinese individuals. Then, we collected 27199 individuals' STRs and geographic data from the literature to investigate the association between STRs and bio-geographic information, and predict geographic information by STRs on additional 1993 unrelated individuals. We found that there was scarcely any association between STRs with studied facial characteristics. Although allele19 in D2S1338 and allele 18 in FGA (P = 0.0032, P = 0.0030, respectively after Bonferroni correction) showed statistical significance, the prediction effectiveness was very low. For the STRs and bio-geographic information, the principal component analysis showed the first three components could explain 87.7% of the variance, but the prediction accuracy only reached 25.2%. We demonstrated that the forensic phenotypes are usually complex traits, it is hardly possible to uncover phenotypic information by testing only dozens of STR loci.
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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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Jian H, Wang L, Lv M, Tan Y, Zhang R, Qu S, Wang J, Zha L, Zhang L, Liang W. A Novel SNP-STR System Based on a Capillary Electrophoresis Platform. Front Genet 2021; 12:636821. [PMID: 33613649 PMCID: PMC7893108 DOI: 10.3389/fgene.2021.636821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
Various compound markers encompassing two or more variants within a small region can be regarded as generalized microhaplotypes. Many of these markers have been investigated for various forensic purposes, such as individual identification, deconvolution of DNA mixtures, or forensic ancestry inference. SNP-STR is a compound biomarker composed of a single nucleotide polymorphism (SNP) and a closely linked short tandem repeat polymorphism (STR), and possess the advantages of both SNPs and STRs. In addition, in conjunction with a polymerase chain reaction (PCR) technique based on the amplification refractory mutation system (ARMS), SNP-STRs can be used for forensic unbalanced DNA mixture analysis based on capillary electrophoresis (CE), which is the most commonly used platform in worldwide forensic laboratories. Our previous research reported 11 SNP-STRs, but few of them are derived from the commonly used STR loci, for which existing STR databases can be used as a reference. For maximum compatibility with existing DNA databases, in this study, we screened 18 SNP-STR loci, of which 14 were derived from the expanded CODIS core loci set. Stable and sensitive SNP-STR multiplex PCR panels based on the CE platform were established. Assays on simulated two-person DNA mixtures showed that all allele-specific primers could detect minor DNA components in 1:500 mixtures. Population data based on 113 unrelated Chengdu Han individuals were investigated. A Bayesian framework was developed for the likelihood ratio (LR) evaluation of SNP-STR profiling results obtained from two-person mixtures. Furthermore, we report on the first use of SNP-STRs in casework to show the advantages and limitations for use in practice. Compared to 2.86 × 103 for autosomal STR kits, the combined LR reached 7.14 × 107 using the SNP-STR method in this casework example.
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Affiliation(s)
- Hui Jian
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yu Tan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ranran Zhang
- 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
| | - Jijun Wang
- HI-TECH Industrial Sub-Branch of Chengdu Municipal Public Security Bureau, Chengdu, China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lin Zhang
- 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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15
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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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16
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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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17
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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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18
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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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19
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Standage DS, Mitchell RN. MicroHapDB: A Portable and Extensible Database of All Published Microhaplotype Marker and Frequency Data. Front Genet 2020; 11:781. [PMID: 32849792 PMCID: PMC7427474 DOI: 10.3389/fgene.2020.00781] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/30/2020] [Indexed: 02/03/2023] Open
Abstract
Microhaplotypes are the subject of significant interest in the forensics community as a promising multi-purpose forensic DNA marker for human identification. Microhaplotype markers are composed of multiple SNPs in close proximity, such that a single NGS read can simultaneously genotype the individual SNPs and phase them in aggregate to determine the associated donor haplotype. Abundant throughout the human genome, numerous recent studies have sought to discover and rank microhaplotype markers according to allelic diversity within and among populations. Microhaplotypes provide an appealing alternative to STR markers for human identification and mixture deconvolution, but can also be optimized for ancestry inference or combined with phenotype SNPs for prediction of externally visible characteristics in a multiplex NGS assay. Designing and evaluating panels of microhaplotypes is complicated by the lack of a convenient database of all published data, as well as the lack of population allele frequency data spanning disparate marker collections. We present MicroHapDB, a comprehensive database of published microhaplotype marker and frequency data, as a tool to advance the development of microhaplotype-based human forensics capabilities. We also present population allele frequencies derived from 26 global population samples for all microhaplotype markers published to date, facilitating the design and interpretation of custom multi-source panels. We submit MicroHapDB as a resource for community members engaged in marker discovery, population studies, assay development, and panel and kit design.
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Affiliation(s)
- Daniel S Standage
- National Bioforensic Analysis Center, National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, United States
| | - Rebecca N Mitchell
- National Bioforensic Analysis Center, National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, United States
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20
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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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21
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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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22
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Zhang R, Tan Y, Jian H, Qu S, Liu Y, Zhu J, Wang L, Lv M, Liao M, Zhang L, Yang F, Liang W. A new approach to detect a set of SNP-SNP markers: Combining ARMS-PCR with SNaPshot technology. Electrophoresis 2020; 41:1189-1197. [PMID: 32333411 DOI: 10.1002/elps.202000009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/10/2020] [Accepted: 04/17/2020] [Indexed: 12/28/2022]
Abstract
Microhaplotypes are a new promising type of forensic genetic marker. Without the interference of stutter and high mutation rates as for STRs, and with short amplification lengths and a higher degree of polymorphism than single SNP, microhaplotypes composed of two SNPs, SNP-SNP, have a strong application potential. Currently, the most common method to detect microhaplotypes is massive parallel sequencing. However, the cost and extensive use of instruments limit its wide application in forensic laboratories. In this study, we screened 23 new SNP-SNP loci and established a new detection method by combining a multiplex amplification refractory mutation system-based PCR (ARMS-PCR) and SNaPshot technology based on CE. First, we introduced an additional deliberate mismatch at the antepenultimate base from the 3' end of primers when designing ARMS-PCR for SNP 1 (the first SNP of the SNP-SNP). Then, single base extension primers for SNaPshot assay were designed next to the position of SNP 2 (the second SNP). Finally, 15 loci were successfully built into four panels and these loci showed a relatively high level of polymorphism in the Southwest Chinese Han population. All the loci had an average probability of informative genotypes (I value) of 0.319 and a combined discrimination power of 0.999999999. Therefore, this new detection system will provide a valuable supplement to current methods.
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Affiliation(s)
- Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Hui Jian
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yuqing Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jing Zhu
- Department of Forensic Science and Technology, Sichuan Police College, Luzhou, Sichuan, P. R. China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Chengdu, Sichuan, P. R. China
| | - Meili Lv
- Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Fan Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Chengdu, Sichuan, P. R. China.,Department of Ultrasonography, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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23
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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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24
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Building a custom large-scale panel of novel microhaplotypes for forensic identification using MiSeq and Ion S5 massively parallel sequencing systems. Forensic Sci Int Genet 2019; 45:102213. [PMID: 31835179 DOI: 10.1016/j.fsigen.2019.102213] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
A large number of new microhaplotype loci were identified in the human genome by applying a directed search with selection criteria emphasizing short haplotype length (<120 nucleotides) and maximum levels of polymorphism in the composite SNPs. From these searches, 107 autosomal microhaplotypes and 11 X chromosome microhaplotypes were selected, with well-spaced autosomal positions to ensure their independence in relationship tests. The 118 microhaplotypes were assembled into a single multiplex assay for the analysis of forensic DNA with massively parallel sequencing (MPS). A single AmpliSeq-adapted primer set was made for Illumina MiSeq and Thermo Fisher Ion S5 MPS platforms and the performance of the assay was comprehensively evaluated in both systems. Five microhaplotypes showed critical sequencing failures in both MPS platforms and were removed, while a further 13 required manual checks and the application of sequence quality thresholds in one or both systems to ensure the successful analysis of low-level DNA in these loci. The targeting of short microhaplotype spans during marker selection, with an average length of 51 nucleotides in the 118 loci, led to a high level of sensitivity for the panel when sequencing the very degraded DNA typically encountered in forensic casework and the identification of missing persons.
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25
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Bennett L, Oldoni F, Long K, Cisana S, Madella K, Wootton S, Chang J, Hasegawa R, Lagacé R, Kidd KK, Podini D. Mixture deconvolution by massively parallel sequencing of microhaplotypes. Int J Legal Med 2019; 133:719-729. [PMID: 30758713 DOI: 10.1007/s00414-019-02010-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
Short tandem repeat polymorphisms (STRs) are the standard markers for forensic human identification. STRs are highly polymorphic loci analyzed using a direct PCR-to-CE (capillary electrophoresis) approach. However, STRs have limitations particularly when dealing with complex mixtures. These include slippage of the polymerase during amplification causing stutter fragments that can be indistinguishable from minor contributor alleles, preferential amplification of shorter alleles, and limited number of loci that can be effectively co-amplified with CE. Massively parallel sequencing (MPS), by enabling a higher level of multiplexing and actual sequencing of the DNA, provides forensic practitioners an increased power of discrimination offered by the sequence of STR alleles and access to new sequence-based markers. Microhaplotypes (i.e., microhaps or MHs) are emerging multi-allelic loci of two or more SNPs within < 300 bp that are highly polymorphic, have alleles all of the same length, and do not generate stutter fragments. The growing number of loci described in the literature along with initial mixture investigations supports the potential for microhaps to aid in mixture interpretation and the purpose of this study was to demonstrate that practically. A panel of 36 microhaplotypes, selected from a set of over 130 loci, was tested with the Ion S5™ MPS platform (Thermo Fisher Scientific) on single-source samples, synthetic two-to-six person mixtures at different concentrations/contributor ratios, and on crime scene-like samples. The panel was tested both in multiplex with STRs and SNPs and individually. The analysis of single-source samples showed that the allele coverage ratio across all loci was 0.88 ± 0.08 which is in line with the peak height ratio of STR alleles in CE. In mixture studies, results showed that the input DNA can be much higher than with conventional CE, without the risk of oversaturating the detection system, enabling an increased sensitivity for the minor contributor in imbalanced mixtures with abundant amounts of DNA. Furthermore, the absence of stutter fragments simplifies the interpretation. On casework-like samples, MPS of MHs enabled the detection of a higher number of alleles from minor donors than MPS and CE of STRs. These results demonstrated that MPS of microhaplotypes can complement STRs and enhance human identification practices when dealing with complex imbalanced mixtures.
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Affiliation(s)
- Lindsay Bennett
- Metro Nashville Police Department Crime Laboratory, 400 Myatt Drive, Madison, TN, 37115, USA
| | - Fabio Oldoni
- The Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, D.C., 20007, USA
| | - Kelly Long
- The Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, D.C., 20007, USA
| | - Selena Cisana
- The Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, D.C., 20007, USA
| | - Katrina Madella
- The Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, D.C., 20007, USA
| | - Sharon Wootton
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, San Francisco, CA, 94080, USA
| | - Joseph Chang
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, San Francisco, CA, 94080, USA
| | - Ryo Hasegawa
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, San Francisco, CA, 94080, USA
| | - Robert Lagacé
- Thermo Fisher Scientific, 180 Oyster Point Boulevard, San Francisco, CA, 94080, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Daniele Podini
- The Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, D.C., 20007, USA.
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Oldoni F, Kidd KK, Podini D. Microhaplotypes in forensic genetics. Forensic Sci Int Genet 2018; 38:54-69. [PMID: 30347322 DOI: 10.1016/j.fsigen.2018.09.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 01/28/2023]
Abstract
Microhaplotype loci (microhaps, MHs) are a novel type of molecular marker of less than 300 nucleotides, defined by two or more closely linked SNPs associated in multiple allelic combinations. The value of these markers is enhanced by massively parallel sequencing (MPS), which allows the sequencing of both parental haplotypes at each of the many multiplexed loci. This review describes the features of these multi-SNP markers and documents their value in forensic genetics, focusing on individualization, biogeographic ancestry inference, and mixture deconvolution. Foreseeable applications also include missing person identification, relationship testing, and medical diagnostic applications. The technique is not restricted to humans.
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Affiliation(s)
- Fabio Oldoni
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States
| | - Kenneth K Kidd
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT, 06520, United States
| | - Daniele Podini
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States.
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