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Xue J, Tan M, Wu Q, Zheng Y, Liu G, Zhang R, Chen D, Xiao Y, Liao M, Lv M, Qu S, Liang W, Zhang L. MHBase: A comprehensive database of short microhaplotypes for advancing forensic genetic analysis. Forensic Sci Int Genet 2024; 71:103062. [PMID: 38795552 DOI: 10.1016/j.fsigen.2024.103062] [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: 12/12/2023] [Revised: 04/02/2024] [Accepted: 05/14/2024] [Indexed: 05/28/2024]
Abstract
Microhaplotypes (MHs) were first recommended by Prof. Kidd for use in forensics because they can improve human identification, kinship analysis, mixture deconvolution, and ancestry prediction. Since their introduction, extensive research has demonstrated the advantages of MHs in forensic applications and provided useful data for different populations. Currently, two databases, ALFRED (ALlele FREquency Database) and MicroHapDB (MicroHaplotype DataBase), house the published MH information and population data. We previously constructed a single nucleotide polymorphism SNP-SNP MH database (D-SNPsDB) of MHs within 50 bp on the whole human genome for 26 populations integrating basic data such as physical genome positions, mapping of variant identifiers (rsIDs), allele frequencies, and basic variant information. Building upon the previous research, we further selected MHs containing at least two variants (SNPs and/or insertions/deletions [InDels]) within a short DNA fragment (≤ 50 bp) in 26 populations based on the 1000 Genomes Project dataset (Phase 3) to construct a more comprehensive database. Subsequently, we established a user-friendly website that allows users to search the MH database (MHBase) based on their research objectives and study population to find suitable loci and provides other functions such as querying reported loci, performing online calculations using the PHASE software, and calculating ancestral-related parameters. The loci in the database are classified as SNP-based MHs, which include only SNPs, and InDel-including MHs, which contain at least one InDel. Here, we provide a detailed overview of the MHBase and an analysis of shared loci at the global and continental levels, ancestral markers, the genetic distance within loci, and mapping with the genome annotation file. The website is an accessible and useful tool for researchers engaged in marker discovery, population studies, assay development, and panel design.
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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, Sichuan 610041, China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Meli Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 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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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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Damour G, Mauffrey F, Hall D. Identification and characterization of novel DIP-STRs from whole-genome sequencing data. Forensic Sci Int Genet 2023; 64:102849. [PMID: 36827792 DOI: 10.1016/j.fsigen.2023.102849] [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: 11/29/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
In an attempt to enhance forensic DNA mixture deconvolution several alternative DNA typing approaches have been developed. Among these, DIP-STR compound markers can resolve extremely unbalanced two-source DNA mixtures of same-or-opposite sex donors, up to a 1:1000 minor:major DNA ratio. A forensic set of 10 markers was validated for casework and a larger set of 23 DIP-STRs has proven suitable to biogeographic ancestry inference and for prenatal paternity testing. Yet, to promote the widespread use of this original approach, more markers and multiplex panels need to be developed. To this end, here we describe an extended set of forensic DIP-STRs identified using currently available whole-genome sequencing datasets. Complete lists of Indels and STRs were obtained from reported frequencies of genetic variants of 76,156 genomes. About 3000 identified DIP-STRs candidates were shorter than 200 bp and 500 showed high haplotype variability estimated using the genotypes of individuals homozygous for the DIP or the STR. Here, we present 23 additional DIP-STRs validated for sensitivity, specificity and Swiss population variability. Finally, a set of 30 markers comprising seven previously validated ones is proposed for the prospective development of a forensic DIP-STR multiplex panel.
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Affiliation(s)
- Géraldine Damour
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000 Lausanne, Switzerland
| | - Florian Mauffrey
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000 Lausanne, Switzerland
| | - Diana Hall
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000 Lausanne, Switzerland.
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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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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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Alladio E, Poggiali B, Cosenza G, Pilli E. Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field. Sci Rep 2022; 12:8974. [PMID: 35643723 PMCID: PMC9148302 DOI: 10.1038/s41598-022-12903-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/13/2022] [Indexed: 11/24/2022] Open
Abstract
The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring their genealogy, and the capability to distinguish biogeographic information about population groups and subgroups via DNA analysis plays an essential role in several fields such as in forensics. In fact, for investigative and intelligence purposes, it is beneficial to inference the biogeographical origins of perpetrators of crimes or victims of unsolved cold cases when no reference profile from perpetrators or database hits for comparative purposes are available. Current approaches for biogeographical ancestry estimation using SNPs data are usually based on PCA and Structure software. The present study provides an alternative method that involves multivariate data analysis and machine learning strategies to evaluate BGA discriminating power of unknown samples using different commercial panels. Starting from 1000 Genomes project, Simons Genome Diversity Project and Human Genome Diversity Project datasets involving African, American, Asian, European and Oceania individuals, and moving towards further and more geographically restricted populations, powerful multivariate techniques such as Partial Least Squares-Discriminant Analysis (PLS-DA) and machine learning techniques such as XGBoost were employed, and their discriminating power was compared. PLS-DA method provided more robust classifications than XGBoost method, showing that the adopted approach might be an interesting tool for forensic experts to infer BGA information from the DNA profile of unknown individuals, but also highlighting that the commercial forensic panels could be inadequate to discriminate populations at intra-continental level.
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Affiliation(s)
- Eugenio Alladio
- Department of Chemistry, University of Turin, Turin, Italy.,Centro Regionale Antidoping e di Tossicologia "A. Bertinaria", Orbassano, Torino, Italy
| | - Brando Poggiali
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Giulia Cosenza
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Elena Pilli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy.
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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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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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Wen D, Sun S, Liu Y, Li J, Yang Z, Kureshi A, Fu Y, Li H, Jiang B, Jin C, Cai J, Zha L. Considering the flanking region variants of nonbinary SNP and phenotype-informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications. Electrophoresis 2021; 42:1115-1126. [PMID: 33483973 DOI: 10.1002/elps.202000341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 12/15/2022]
Abstract
The flanking region variants of nonbinary SNPs and phenotype-informative SNPs (piSNPs) have been observed, which may greatly improve the discriminative ability after constituting microhaplotype. In this study, 30 microhaplotype loci based on the nonbinary SNPs and piSNPs (shown to be related to phenotypes such as hair and eye color) were selected. Genotyping were conducted on 100 unrelated northern Han Chinese, and the 26 populations from the 1000 Genome Project were also included for comparison of populations differentiation. The simulated study was conducted for evaluating the efficiency of kinship testing. These 30 microhaplotype loci we selected had good polymorphism, with a mean effective number of alleles (Ae) of 3.46. The average Ae increase was 1.27 compared with the target SNPs. The populations from the five regions worldwide could also be distinguished using these loci. The results of kinship testing showed that these microhaplotype loci had the similar ability as 15 STR loci of AmpFlSTRR IdentifilerR PCR Amplification Kit to identify the biological parent and a stronger ability to exclude the nonbiological parents. So, these 30 microhaplotype loci may be multifunctional for forensic application, including the ability of personal identification and kinship testing equivalent to 15 STR loci, and the power of ancestry inference for distinguishing the main intercontinental population. Moreover, our selected phenotypic microhaplotype loci may theoretically have phenotype prediction capabilities. But the phenotype prediction efficiency of these phenotypic microhaplotype loci may be worse than that of piSNPs and the detailed prediction accuracy of different populations needs to be further studied.
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Affiliation(s)
- Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Shule Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Ying Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Zedeng Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Aliye Kureshi
- School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, P. R. China
| | - Yan Fu
- Huazhi Biotech Co., Ltd, Changsha, P. R. China
| | - Henan Li
- Microanaly Gene Technologies Co., Ltd, Hefei, P. R. China
| | - Bowei Jiang
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, P. R. China
| | - Chuan Jin
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, P. R. China
| | - Jifeng Cai
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
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