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Gettings KB, Tillmar A, Sturk-Andreaggi K, Marshall C. Review of SNP assays for disaster victim identification: Cost, time, and performance information for decision-makers. J Forensic Sci 2024; 69:1546-1557. [PMID: 39021258 DOI: 10.1111/1556-4029.15585] [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: 05/22/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
In mass disaster events, forensic DNA laboratories may be called upon to quickly pivot their operations toward identifying bodies and reuniting remains with family members. Ideally, laboratories have considered this possibility in advance and have a plan in place. Compared with traditional short tandem repeat (STR) typing, single nucleotide polymorphisms (SNPs) may be better suited to these disaster victim identification (DVI) scenarios due to their small genomic target size, resulting in an improved success rate in degraded DNA samples. As the landscape of technology has shifted toward DNA sequencing, many forensic laboratories now have benchtop instruments available for massively parallel sequencing (MPS), facilitating this operational pivot from routine forensic STR casework to DVI SNP typing. Herein, we present the commercially available SNP sequencing assays amenable to DVI, we use data simulations to explore the potential for kinship prediction from SNP panels of varying sizes, and we give an example DVI scenario as context for presenting the matrix of considerations: kinship predictive potential, cost, and throughput of current SNP assay options. This information is intended to assist laboratories in choosing a SNP system for disaster preparedness.
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Affiliation(s)
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 10 Defense Health Agency, Dover Air Force Base, Dover, Delaware, USA
- SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, Virginia, USA
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 10 Defense Health Agency, Dover Air Force Base, Dover, Delaware, USA
- Forensic Science Program, The Pennsylvania State University, State College, Pennsylvania, USA
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2
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Wang X, Huang M, Budowle B, Ge J. TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads. Front Genet 2023; 14:1227176. [PMID: 37533432 PMCID: PMC10390829 DOI: 10.3389/fgene.2023.1227176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/13/2023] [Indexed: 08/04/2023] Open
Abstract
Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.
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Affiliation(s)
- Xuewen Wang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Meng Huang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
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3
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Elwick K, Rydzak P, Robertson JM. Evaluation of Library Preparation Workflows and Applications to Different Sample Types Using the PowerSeq ® 46GY System with Massively Parallel Sequencing. Genes (Basel) 2023; 14:genes14050977. [PMID: 37239337 DOI: 10.3390/genes14050977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
This project evaluated the prototype PowerSeq® 46GY System using donor DNA and casework-type samples. The goal of this study was to determine whether modifications to the manufacturer's protocol could increase read coverage and improve sample results. Buccal and casework-type libraries were prepared using the TruSeq® DNA PCR-Free HT kit or the KAPA HyperPrep kit. Both kits were evaluated unmodified, and by substituting AMPure® XP beads for the beads of the most optimal kit. Two qPCR kits, the PowerSeq® Quant MS System and KAPA Library Quantification Kit, were also evaluated along with a KAPA size-adjustment workbook, which was compared as a third quantification method. Libraries were sequenced using the MiSeq® FGx and data were analyzed with STRait Razor. Results suggested that all three quantification methods overestimated library concentration, but the PowerSeq kit was most accurate. Samples prepared with the TruSeq library kit provided the highest coverage and the fewest instances of dropout and below-threshold alleles compared with the KAPA kit. Additionally, all bone and hair samples demonstrated full profile completeness, with bone samples yielding a higher average coverage than hair samples. Overall, our study demonstrated that the 46GY manufacturer's protocol produced the best quality results compared to alternative library preparation options.
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Affiliation(s)
- Kyleen Elwick
- Visiting Scientist Program, Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Patrick Rydzak
- Visiting Scientist Program, Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - James M Robertson
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA 22135, USA
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Poethe SS, Holtel J, Biermann JP, Riemer T, Grabmüller M, Madea B, Thiele R, Jäger R. Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples. Int J Mol Sci 2023; 24:ijms24043382. [PMID: 36834791 PMCID: PMC9960623 DOI: 10.3390/ijms24043382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Forensic DNA profiles are established by multiplex PCR amplification of a set of highly variable short tandem repeat (STR) loci followed by capillary electrophoresis (CE) as a means to assign alleles to PCR products of differential length. Recently, CE analysis of STR amplicons has been supplemented by high-throughput next generation sequencing (NGS) techniques that are able to detect isoalleles bearing sequence polymorphisms and allow for an improved analysis of degraded DNA. Several such assays have been commercialised and validated for forensic applications. However, these systems are cost-effective only when applied to high numbers of samples. We report here an alternative, cost-efficient shallow-sequence output NGS assay called maSTR assay that, in conjunction with a dedicated bioinformatics pipeline called SNiPSTR, can be implemented with standard NGS instrumentation. In a back-to-back comparison with a CE-based, commercial forensic STR kit, we find that for samples with low DNA content, with mixed DNA from different individuals, or containing PCR inhibitors, the maSTR assay performs equally well, and with degraded DNA is superior to CE-based analysis. Thus, the maSTR assay is a simple, robust and cost-efficient NGS-based STR typing method applicable for human identification in forensic and biomedical contexts.
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Affiliation(s)
- Sara-Sophie Poethe
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Julia Holtel
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Jan-Philip Biermann
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Trine Riemer
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Melanie Grabmüller
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Burkhard Madea
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Ralf Thiele
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Computer Science Department, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Richard Jäger
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany
- Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Correspondence:
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Cheng K, Bright JA, Kelly H, Liu YY, Lin MH, Kruijver M, Taylor D, Buckleton J. Developmental validation of STRmix™ NGS, a probabilistic genotyping tool for the interpretation of autosomal STRs from forensic profiles generated using NGS. Forensic Sci Int Genet 2023; 62:102804. [PMID: 36370677 DOI: 10.1016/j.fsigen.2022.102804] [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: 08/29/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
We describe the developmental validation of the probabilistic genotyping software - STRmix™ NGS - developed for the interpretation of forensic DNA profiles containing autosomal STRs generated using next generation sequencing (NGS) also known as massively parallel sequencing (MPS) technologies. Developmental validation was carried out in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) Guidelines for the Validation of Probabilistic Genotyping Systems and the International Society for Forensic Genetics (ISFG) recommendations and included sensitivity and specificity testing, accuracy, precision, and the interpretation of case-types samples. The results of developmental validation demonstrate the appropriateness of the software for the interpretation of profiles developed using NGS technology.
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Affiliation(s)
- Kevin Cheng
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand.
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Hannah Kelly
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Yao-Yuan Liu
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Meng-Han Lin
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Maarten Kruijver
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
| | - Duncan Taylor
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - John Buckleton
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
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6
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Wang X, Budowle B, Ge J. USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences. BMC Bioinformatics 2022; 23:497. [PMID: 36402991 PMCID: PMC9675219 DOI: 10.1186/s12859-022-05021-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/29/2022] [Indexed: 11/21/2022] Open
Abstract
Background Tandem repeats (TR), highly variable genomic variants, are widely used in individual identification, disease diagnostics, and evolutionary studies. The recent advances in sequencing technologies and bioinformatic tools facilitate calling TR haplotypes genome widely. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision in characterizing TR haplotypes. The need to identify the differences at the single nucleotide level between or among TR haplotypes with an easy-use bioinformatic tool is essential. Results In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which takes TR haplotype output from existing tools to perform allele size conversion, sequence comparison of haplotypes, figure plotting, comparison for allele distribution, and interactive visualization. An exemplary application of USAT for analysis of the CODIS core STR loci for DNA forensics with benchmarking human individuals demonstrated the capabilities of USAT. USAT has user-friendly graphic interfaces and runs fast in major computing operating systems with parallel computing enabled. Conclusion USAT is a user-friendly bioinformatics software for interpretation, visualization, and comparisons of TRs. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-05021-1.
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Affiliation(s)
- Xuewen Wang
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA
| | - Bruce Budowle
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA ,grid.266871.c0000 0000 9765 6057Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX USA
| | - Jianye Ge
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA ,grid.266871.c0000 0000 9765 6057Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX USA
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7
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Guo F, Lang Y, Long G, Liu Z, Jing G, Zhou Y, Zhang B, Yu S. Ion Torrent TM Genexus TM Integrated Sequencer and ForeNGS Analysis Software—an automatic NGS-STR workflow from DNA to profile for forensic science. Forensic Sci Int Genet 2022; 61:102753. [DOI: 10.1016/j.fsigen.2022.102753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/03/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
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8
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Hall CL, Kesharwani RK, Phillips NR, Planz JV, Sedlazeck FJ, Zascavage RR. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device. Forensic Sci Int Genet 2021; 56:102629. [PMID: 34837788 DOI: 10.1016/j.fsigen.2021.102629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/28/2021] [Accepted: 11/01/2021] [Indexed: 01/23/2023]
Abstract
The high variability characteristic of short tandem repeat (STR) markers is harnessed for human identification in forensic genetic analyses. Despite the power and reliability of current typing techniques, sequence-level information both within and around STRs are masked in the length-based profiles generated. Forensic STR typing using next generation sequencing (NGS) has therefore gained attention as an alternative to traditional capillary electrophoresis (CE) approaches. In this proof-of-principle study, we evaluate the forensic applicability of the newest and smallest NGS platform available - the Oxford Nanopore Technologies (ONT) MinION device. Although nanopore sequencing on the handheld MinION offers numerous advantages, including low startup cost and on-site sample processing, the relatively high error rate and lack of forensic-specific analysis software has prevented accurate profiling across STR panels in previous studies. Here we present STRspy, a streamlined method capable of producing length- and sequence-based STR allele designations from noisy, error-prone third generation sequencing reads. To assess the capabilities of STRspy, seven reference samples (female: n = 2; male: n = 5) were amplified at 15 and 30 PCR cycles using the Promega PowerSeq 46GY System and sequenced on the ONT MinION device in triplicate. Basecalled reads were then processed with STRspy using a custom database containing alleles reported in the STRSeq BioProject NIST 1036 dataset. Resultant STR allele designations and flanking region single nucleotide polymorphism (SNP) calls were compared to the manufacturer-validated genotypes for each sample. STRspy generated robust and reliable genotypes across all autosomal STR loci amplified with 30 PCR cycles, achieving 100% concordance based on both length and sequence. Furthermore, we were able to identify flanking region SNPs in the 15-cycle dataset with > 90% accuracy. These results demonstrate that when analyzed with STRspy ONT reads can reveal additional variation in and around STR loci depending on read coverage. As the first and only third generation sequencing platform-specific method to successfully profile the entire panel of autosomal STRs amplified by a commercially available multiplex, STRspy significantly increases the feasibility of nanopore sequencing in forensic applications.
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Affiliation(s)
- Courtney L Hall
- Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, 3400 Camp Bowie Blvd, Fort Worth, TX 76107, USA.
| | - Rupesh K Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Nicole R Phillips
- Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, 3400 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - John V Planz
- Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, 3400 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Roxanne R Zascavage
- Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, 3400 Camp Bowie Blvd, Fort Worth, TX 76107, USA; Department of Criminology and Criminal Justice, University of Texas at Arlington, 701 S Nedderman Dr, Arlington, TX 76109, USA
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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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Reverse complement-PCR, an innovative and effective method for multiplexing forensically relevant single nucleotide polymorphism marker systems. Biotechniques 2021; 71:484-489. [PMID: 34350776 DOI: 10.2144/btn-2021-0031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA analyses from challenging samples such as touch evidence, hairs and skeletal remains push the limits of the current forensic DNA typing technologies. Reverse complement PCR (RC-PCR) is a novel, single-step PCR target enrichment method adapted to amplify degraded DNA. The sample preparation process involves a limited number of steps, decreasing the labor required for library preparation and reducing the possibility of contamination due to less sample manipulation. These features of the RC-PCR make the technology a unique application to successfully target single nucleotide polymorphisms (SNPs) in fragmented and low copy number DNA and yield results from samples in which no or limited data are obtained with standard DNA typing methods. The developed RC-PCR short amplicon 85 SNP-plex panel is a substantial improvement over the previously reported 27-plex RC-PCR multiplex that will provide higher discrimination power for challenging DNA sample analyses.
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Moura-Neto R, King JL, Mello I, Dias V, Crysup B, Woerner AE, Budowle B, Silva R. Evaluation of Promega PowerSeq™ Auto/Y systems prototype on an admixed sample of Rio de Janeiro, Brazil: Population data, sensitivity, stutter and mixture studies. Forensic Sci Int Genet 2021; 53:102516. [PMID: 33878618 DOI: 10.1016/j.fsigen.2021.102516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/06/2021] [Accepted: 03/29/2021] [Indexed: 02/01/2023]
Abstract
Forensic DNA typing typically relies on the length-based (LB) separation of PCR products containing short tandem repeat loci (STRs). Massively parallel sequencing (MPS) elucidates an additional level of STR motif and flanking region variation. Also, MPS enables simultaneous analysis of different marker-types - autosomal STRs, SNPs for lineage and identification purposes, reducing both the amount of sample used and the turn-around-time of analysis. Therefore, MPS methodologies are being considered as an additional tool in forensic genetic casework. The PowerSeq™ Auto/Y System (Promega Corp), a multiplex forensic kit for MPS, enables analysis of the 22 autosomal STR markers (plus Amelogenin) from the PowerPlex® Fusion 6C kit and 23 Y-STR markers from the PowerPlex® Y23 kit. Population data were generated from 140 individuals from an admixed sample from Rio de Janeiro, Brazil. All samples were processed according to the manufacturers' recommended protocols. Raw data (FastQ) were generated for each indexed sample and analyzed using STRait Razor v2s and PowerSeqv2.config file. The subsequent population data showed the largest increase in expected heterozygosity (23%), from LB to sequence-based (SB) analyses at the D5S818 locus. Unreported allele was found at the D21S11 locus. The random match probability across all loci decreased from 5.9 × 10-28 to 7.6 × 10-33. Sensitivity studies using 1, 0.25, 0.062 and 0.016 ng of DNA input were analyzed in triplicate. Full Y-STR profiles were detected in all samples, and no autosomal allele drop-out was observed with 62 pg of input DNA. For mixture studies, 1 ng of genomic DNA from a male and female sample at 1:1, 1:4, 1:9, 1:19 and 1:49 proportions were analyzed in triplicate. Clearly resolvable alleles (i.e., no stacking or shared alleles) were obtained at a 1:19 male to female contributor ratio. The minus one stutter (-1) increased with the longest uninterrupted stretch (LUS) allele size reads and according to simple or compound/complex repeats. The haplotype-specific stutter rates add more information for mixed samples interpretation. These data support the use of the PowerSeqTM Auto/Y systems prototype kit (22 autosomal STR loci, 23 Y-STR loci and Amelogenin) for forensic genetics applications.
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Affiliation(s)
- Rodrigo Moura-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Isadora Mello
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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