1
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Sidstedt M, Gynnå AH, Kiesler KM, Jansson L, Steffen CR, Håkansson J, Johansson G, Österlund T, Bogestål Y, Tillmar A, Rådström P, Ståhlberg A, Vallone PM, Hedman J. Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method. Forensic Sci Int Genet 2024; 71:103047. [PMID: 38598919 DOI: 10.1016/j.fsigen.2024.103047] [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: 11/01/2023] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1-15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.
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Affiliation(s)
- Maja Sidstedt
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden
| | - Arvid H Gynnå
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden
| | - Kevin M Kiesler
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Linda Jansson
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden
| | - Carolyn R Steffen
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Joakim Håkansson
- RISE Unit of Biological Function, Division Materials and Production, Box 857, Borås SE-501 15, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg SE-405 30, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Gustav Johansson
- SIMSEN Diagnostics, Sahlgrenska Science Park, Gothenburg, Sweden
| | - Tobias Österlund
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, Gothenburg 41390, Sweden; Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 41390, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland 41390, Sweden
| | - Yalda Bogestål
- RISE Unit of Biological Function, Division Materials and Production, Box 857, Borås SE-501 15, Sweden
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping SE-587 58, Sweden
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden
| | - Anders Ståhlberg
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, Gothenburg 41390, Sweden; Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 41390, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland 41390, Sweden
| | - Peter M Vallone
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Johannes Hedman
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden.
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2
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Huang Y, Wang M, Liu C, He G. Comprehensive landscape of non-CODIS STRs in global populations provides new insights into challenging DNA profiles. Forensic Sci Int Genet 2024; 70:103010. [PMID: 38271830 DOI: 10.1016/j.fsigen.2024.103010] [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: 11/27/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
The worldwide implementation of short tandem repeats (STR) profiles in forensic genetics necessitated establishing and expanding the CODIS core loci set to facilitated efficient data management and exchange. Currently, the mainstay CODIS STRs are adopted in most general-purpose forensic kits. However, relying solely on these loci failed to yield satisfactory results for challenging tasks, such as bio-geographical ancestry inference, complex DNA mixture profile interpretation, and distant kinship analysis. In this context, non-CODIS STRs are potent supplements to enhance the systematic discriminating power, particularly when combined with the high-throughput next-generation sequencing (NGS) technique. Nevertheless, comprehensive evaluation on non-CODIS STRs in diverse populations was scarce, hindering their further application in routine caseworks. To address this gap, we investigated genetic variations of 178 historically available non-CODIS STRs from ethnolinguistically different worldwide populations and studied their characteristics and forensic potentials via high-coverage whole genome sequencing (WGS) data. Initially, we delineated the genomic properties of these non-CODIS markers through sequence searching, repeat structure scanning, and manual inspection. Subsequent population genetics analysis suggested that these non-CODIS STRs had comparable polymorphism levels and forensic utility to CODIS STRs. Furthermore, we constructed a theoretical next-generation sequencing (NGS) panel comprising 108 STRs (20 CODIS STRs and 88 non-CODIS STRs), and evaluated its performance in inferring bio-geographical ancestry origins, deconvoluting complex DNA mixtures, and differentiating distant kinships using real and simulated datasets. Our findings demonstrated that incorporating supplementary non-CODIS STRs enabled the extrapolation of multidimensional information from a single STR profile, thereby facilitating the analysis of challenging forensic tasks. In conclusion, this study presents an extensive genomic landscape of forensic non-CODIS STRs among global populations, and emphasized the imperative inclusion of additional polymorphic non-CODIS STRs in future NGS-based forensic systems.
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Affiliation(s)
- Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China.
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China; Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China; Center for Archaeological Science, Sichuan University, Chengdu 610000, China.
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3
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Bodner M, Ballard D, Borsuk LA, King JL, Parson W, Phillips C, Gettings KB. Harmonizing the forensic nomenclature for STR loci D6S474 and DYS612. Forensic Sci Int Genet 2024; 70:103012. [PMID: 38295652 DOI: 10.1016/j.fsigen.2024.103012] [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: 08/10/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 04/01/2024]
Abstract
The autosomal STR D6S474 and the Y-chromosomal STR DYS612 have been reported in multiple ways in the forensic literature, with differences in both the bracketed repeat structures and counting of numerical length-based capillary electrophoresis (CE) alleles. These issues often come to light when STR loci are introduced in commercial assays and results compared with historical publications of allele frequency data, or multiple assays are characterized with reference materials. We review the forensic literature and other relevant information, and provide suggestions for the future treatment of each STR.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - David Ballard
- King's Forensics, King's College London, Franklin-Wilkins Building, London, UK
| | - Lisa A Borsuk
- National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, MD, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Katherine Butler Gettings
- National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, MD, USA.
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4
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Gettings KB, Bodner M, Borsuk LA, King JL, Ballard D, Parson W, Benschop CCG, Børsting C, Budowle B, Butler JM, van der Gaag KJ, Gill P, Gusmão L, Hares DR, Hoogenboom J, Irwin J, Prieto L, Schneider PM, Vennemann M, Phillips C. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on short tandem repeat sequence nomenclature. Forensic Sci Int Genet 2024; 68:102946. [PMID: 39090852 DOI: 10.1016/j.fsigen.2023.102946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 10/14/2023] [Indexed: 08/04/2024]
Abstract
The DNA Commission of the International Society for Forensic Genetics (ISFG) has developed a set of nomenclature recommendations for short tandem repeat (STR) sequences. These recommendations follow the 2016 considerations of the DNA Commission of the ISFG, incorporating the knowledge gained through research and population studies in the intervening years. While maintaining a focus on backward compatibility with the CE data that currently populate national DNA databases, this report also looks to the future with the establishment of recommended minimum sequence reporting ranges to facilitate interlaboratory comparisons, automated solutions for sequence-based allele designations, a suite of resources to support bioinformatic development, guidance for characterizing new STR loci, and considerations for incorporating STR sequences and other new markers into investigative databases.
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Affiliation(s)
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Lisa A Borsuk
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, King's College London, London, United Kingdom
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Corina C G Benschop
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Denmark
| | - Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland; Radford University Forensic Science Institute, Radford University, Radford, VA, USA
| | - John M Butler
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Peter Gill
- Forensic Genetics Research Group, Oslo University Hospital, Oslo, Norway
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Jerry Hoogenboom
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands
| | | | - Lourdes Prieto
- Forensic Sciences Institute Luis Concheiro. University of Santiago de Compostela, Santiago de Compostela, Spain; Comisaría General de Policía Científica, Madrid, Spain
| | - Peter M Schneider
- Institute of Legal Medicine, University of Cologne, Cologne, Germany
| | | | - Christopher Phillips
- Forensic Sciences Institute Luis Concheiro. University of Santiago de Compostela, Santiago de Compostela, Spain
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5
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Sala A, Marino M, Guinudinik A, Marcucci V, Cano H, Rey SV, Bobillo C, Castagnola J, Garrigós-Calivares L, Ginart S, Caputo M, Corach D. Detection of a novel 16.3 variant allele at locus DYS533 in R1b males inhabiting southern South America: A 19-nucleotide insertion explains its origin based on Sanger sequencing results. Forensic Sci Int Genet 2023; 62:102789. [PMID: 36252401 DOI: 10.1016/j.fsigen.2022.102789] [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: 05/31/2022] [Revised: 08/24/2022] [Accepted: 10/07/2022] [Indexed: 12/14/2022]
Abstract
We typed 1541 Y-STR haplotypes from reference samples along forensic casework investigations. In three haplotypes, we detected a variant allele designed as 16.3 at locus DYS533. This was confirmed by amplification using two commercial kits. Sanger sequencing revealing a novel motif corresponding to [TATC]12 repeats with a 19-bp insertion in the flanking upstream region. We propose its origin as an insertion at - 9.1 upstream of the repeat motifs. We searched other local databases and found this allele in various geographical areas of Argentina and neighbouring countries. The haplotypes share a common core of 10 Y-STRs (DYS389-I/13; DYS389-II/30; DYS19/14; DYS481/22; DYS438/12; DYS437/16; DYS635/23; DYS392/13; DYS393/13; GATA H4/11) and belong to the R1b haplogroup. This 16.3 allele is restricted to southern South America, which allows us to propose a local and relatively recent origin. The sequence described herein constitutes a novelty that could be considered in future criteria for the nomenclature of STRs based on massively parallel sequencing.
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Affiliation(s)
- Andrea Sala
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina.
| | - Miguel Marino
- Registro Provincial de Huellas Genéticas Digitalizadas, Lab. de Genética Forense-Ministerio Público Fiscal de Mendoza, Argentina
| | - Alejandra Guinudinik
- Servicio de Biología Molecular del Cuerpo de Investigaciones Fiscales, Ministerio Público de Salta, Argentina
| | - Valeria Marcucci
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Hortensia Cano
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Silvia Vannelli Rey
- Laboratorio Regional de Genética Forense, Ministerio Público de Río Negro, Argentina
| | - Cecilia Bobillo
- Laboratorio de Genética Forense, Ministerio Público de La Pampa, Argentina
| | - Josefina Castagnola
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina
| | - Lucía Garrigós-Calivares
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina
| | - Santiago Ginart
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina
| | - Mariela Caputo
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina
| | - Daniel Corach
- Universidad de Buenos Aires - Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas (SHDG), Junin 956, Ciudad Autónoma de Buenos Aires 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Argentina
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6
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Huang Y, Zhang H, Wei Y, Cao Y, Zhu Q, Li X, Shan T, Dai X, Zhang J. Characterizing the amplification of STR markers in multiplex polymerase chain displacement reaction using massively parallel sequencing. Forensic Sci Int Genet 2023; 62:102802. [PMID: 36332535 DOI: 10.1016/j.fsigen.2022.102802] [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: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 01/15/2023]
Abstract
Polymerase chain displacement reaction (PCDR) showed advantages in forensic low-template DNA analysis with improved amplification efficiency, higher allele detection capacity, and lower stutter artifact than PCR. However, characteristics of STR markers after PCDR amplification remain unclarified for the limited resolving power of capillary electrophoresis (CE). This issue can be addressed by massively parallel sequencing (MPS) technology with higher throughput and discriminability. Here, we developed a multiplex PCDR system including 24 STRs and amelogenin. In addition, a PCR reference was established for comparison. After amplification, products were subjected to PCR-free library construction and sequenced on the Illumina NovaSeq system. We implemented a sequence-matching pipeline to separate different amplicon types of PCDR products from the combination of primers. In the sensitivity test, the PCDR multiplex obtained full STR profiles with as low as 125 pg 2800M control DNA. Based on that, single-source DNA samples were tested. First, highly concordant genotypes were observed among the PCDR multiplex, the PCR reference, and CE-based STR kits. Next, read counts of different PCDR amplicon types were investigated, showing a relative abundance of 78:12:12:1 for the shortest amplicon S, the two medium amplicons M1 and M2, and the longest amplicon L. We also analyzed the stutter artifacts for distinct amplicon types, and the results revealed the reduction of N - 1 and N - 2 contraction stutters, and the increase of N + 1 and N + 2 elongation stutters in PCDR samples. Moreover, we confirmed the feasibility of PCDR for amplifying degraded DNA samples and unbalanced DNA mixtures. Compared to the previous proof of principle study, our work took a further step to characterize the complete profile of STR markers in the PCDR context. Our results suggested that the PCDR-MPS workflow is an effective approach for forensic STR analysis. Corresponding findings in this study may help the development of PCDR-based assays and probabilistic methods in future studies.
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Affiliation(s)
- Yuguo Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Haijun Zhang
- Forensic Science Center of Sichuan Provincial Public Security Department, Chengdu, China
| | - Yifan Wei
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yueyan Cao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiang Zhu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xi Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Tiantian Shan
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xuan Dai
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ji Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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7
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Advancing FDSTools by integrating STRNaming 1.1. Forensic Sci Int Genet 2022; 61:102768. [PMID: 35994887 DOI: 10.1016/j.fsigen.2022.102768] [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: 05/09/2022] [Revised: 07/25/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022]
Abstract
The introduction of massively parallel sequencing in forensic analysis has been facilitated with typing kits, analysis software and allele naming tools such as the ForenSeq DNA Signature Prep (DSP) kit, FDSTools and STRNaming respectively. Here we describe how FDSTools 2.0 with integrated and refined STRNaming nomenclature was validated for implementation under ISO 17025 accreditation for the ForenSeq DSP kit. Newly-added options result in efficient automatic allele calling for the majority of markers while specific settings are applied for 'novel' sequence variants to avoid the calling of remaining variable noise observed in samples sequenced with the ForenSeq DSP kit that seem to arise in the PCR. Genome-wide built-in reference data allows for greatly simplified configuration of allele naming for human targets.
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8
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Tyazhelova TV, Kuznetsova IL, Andreeva TV, Kunizheva SS, Rogaev EI. Application of Massive Parallel Sequencing Technology in Forensics: Comparative Analysis of Sequencing Platforms. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421120127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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9
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An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data. Genes (Basel) 2021; 12:genes12111739. [PMID: 34828345 PMCID: PMC8618049 DOI: 10.3390/genes12111739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022] Open
Abstract
The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing.
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10
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Ralf A, Zandstra D, Weiler N, van Ijcken WFJ, Sijen T, Kayser M. RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates. Forensic Sci Int Genet 2021; 55:102595. [PMID: 34543845 DOI: 10.1016/j.fsigen.2021.102595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) with high mutation rates are recognized as valuable genetic markers for differentiating paternally related men, who typically cannot be separated with standard Y-STRs, and were shown to provide paternal lineage differentiation on a higher resolution level than standard Y-STRs. Both features make Y-STRs with high mutation rates relevant in criminal casework, particularly in sexual assault cases involving highly unbalanced male-female DNA mixtures that often fail autosomal forensic STR profiling for the male donor. Previously, the number of known Y-STRs with mutation rates higher than 10-2 per locus per generation termed rapidly mutating Y-STRs (RM Y-STRs) was limited to 13, which has recently been overcome by the discovery and characterization of 12 additional RM Y-STRs. Here, we present the development and validation of RMplex, an efficient genotyping system for analyzing 30 Y-STRs with high mutation rates, including all currently known RM Y-STRs, using multiplex PCR with capillary electrophoresis (CE) or massively parallel sequencing (MPS), overall targeting a total of 44 male-specific loci. If previously unavailable, repeat number assignations were provided based on newly generated MPS data. Validation tests based on the CE method demonstrated that the results were both repeatable and reproducible, full profiles were achieved with minimal input DNA of 250 pg for RMplex 1 and 100 pg for RMplex 2, and in the presence of inhibitors, or with a surplus of female DNA, the assays performed reasonably well. Application of RMplex to differentiate between paternally related men was exemplified in 32 males belonging to five different paternal pedigrees. Given further successful forensic validation testing, we envision the future application of RMplex in criminal cases where it is suspected, or cannot be excluded, that the crime scene trace originated from a male relatives of the suspect who is highlighted with standard Y-STR matching. Other applications of RMplex are in criminal cases without known suspects to differentiate between male relatives highlighted in familial searching based on standard Y-STR matching.
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Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dion Zandstra
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Natalie Weiler
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands
| | - Wilfred F J van Ijcken
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Titia Sijen
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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