1
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Daca-Roszak P, Fiedorowicz J, Jankowski M, Ciesielka M, Teresiński G, Lipska-Zietkiewicz B, Zietkiewicz E, Grzybowski T, Skonieczna K. The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems. J Appl Genet 2024; 65:559-563. [PMID: 38110828 PMCID: PMC11310223 DOI: 10.1007/s13353-023-00821-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (Nextera XT DNA Library Preparation Kit and Nextera DNA Flex Library Preparation Kit) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems.
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Affiliation(s)
| | - Joanna Fiedorowicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Animal Physiology, Biochemistry and Biostructure, Poznan University of Life Science, Poznan, Poland
| | - Maciej Jankowski
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Marzanna Ciesielka
- Chair and Department of Forensic Medicine, Medical University of Lublin, Lublin, Poland
| | - Grzegorz Teresiński
- Chair and Department of Forensic Medicine, Medical University of Lublin, Lublin, Poland
| | - Beata Lipska-Zietkiewicz
- Centre for Rare Diseases, Medical University of Gdansk, Gdansk, Poland; Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Zietkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland.
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2
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Bali GK, Cuenca D, Wallin J. Effects and considerations of multiplexing ForenSeq Kintelligence libraries with a negative control. Electrophoresis 2024; 45:852-866. [PMID: 38449358 DOI: 10.1002/elps.202300285] [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: 12/07/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024]
Abstract
The negative template control or negative amplification control has been an essential component of the forensic DNA analysis workflow that helps monitor contamination. As such, the inclusion of a negative control in forensic DNA analysis has been a requirement for all laboratories audited under the FBI's Quality Assurance Standards. As massively parallel sequencing (MPS) becomes more conventional in forensic laboratories, considerations for the inclusion of a negative control in every sequencing run can be evaluated. Although the inclusion of a negative control in library preparation and the first sequencing run has a practical function, there is less utility for its inclusion in all subsequent sequencing runs for that library preparation. Although this is universal to all MPS assays, it is most relevant for an assay that has a low sample multiplexing capacity, such as the ForenSeq Kintelligence Kit (Qiagen/Verogen, Inc.). The ForenSeq Kintelligence Kit is an investigative genetic genealogy (IGG) sequencing-based assay that targets 10,230 forensically relevant single-nucleotide polymorphisms. The manufacturer recommends multiplexing 3 libraries per sequencing run, which includes controls. The purpose of this study was to investigate the effect of the inclusion of a negative control in every Kintelligence sequencing run. We observed that the library generated from a negative amplification control will take 7%-14% of the run output. The loss of sequencing space taken by a negative control decreased the available output for DNA-containing samples, leading in some cases to allele or locus dropout and accompanying higher numbers of sixth to seventh order unknown associations in GEDmatch PRO.
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Affiliation(s)
- Gunmeet Kaur Bali
- California Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California, USA
| | - Daniela Cuenca
- California Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California, USA
| | - Jeanette Wallin
- California Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California, USA
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3
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Liu G, Zheng Y, Wu Q, Feng T, Xia Y, Chen D, Ren L, Bai X, Li Q, Chen D, Lv M, Liao M, Liang W, Zhang L, Qu S. Assessment of ForenSeq mtDNA Whole Genome Kit for forensic application. Int J Legal Med 2023; 137:1693-1703. [PMID: 37731065 DOI: 10.1007/s00414-023-03084-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Mitochondrial DNA (mtDNA) is an indispensable genetic marker in forensic genetics. The emergence and development of massively parallel sequencing (MPS) makes it possible to obtain complete mitochondrial genome sequences more quickly and accurately. The study evaluated the advantages and limitations of the ForenSeq mtDNA Whole Genome Kit in the practical application of forensic genetics by detecting human genomic DNA standards and thirty-three case samples. We used control DNA with different amount to determine sensitivity of the assay. Even when the input DNA is as low as 2.5 pg, most of the mitochondrial genome sequences could still be covered. For the detection of buccal swabs and aged case samples (bloodstains, bones, teeth), most samples could achieve complete coverage of mitochondrial genome. However, when ancient samples and hair samples without hair follicles were sequenced by the kit, it failed to obtain sequence information. In general, the ForenSeq mtDNA Whole Genome Kit has certain applicability to forensic low template and degradation samples, and these results provide the data basis for subsequent forensic applications of the assay. The overall detection process and subsequent analysis are easy to standardize, and it has certain application potential in forensic cases.
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Affiliation(s)
- Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Tao Feng
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Yu Xia
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Dan Chen
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Li Ren
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Xiaogang Bai
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Qingqing Li
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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4
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Budowle B, Arnette A, Sajantila A. A cost-benefit analysis for use of large SNP panels and high throughput typing for forensic investigative genetic genealogy. Int J Legal Med 2023; 137:1595-1614. [PMID: 37341834 PMCID: PMC10421786 DOI: 10.1007/s00414-023-03029-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/16/2023] [Indexed: 06/22/2023]
Abstract
Next-generation sequencing (NGS), also known as massively sequencing, enables large dense SNP panel analyses which generate the genetic component of forensic investigative genetic genealogy (FIGG). While the costs of implementing large SNP panel analyses into the laboratory system may seem high and daunting, the benefits of the technology may more than justify the investment. To determine if an infrastructural investment in public laboratories and using large SNP panel analyses would reap substantial benefits to society, a cost-benefit analysis (CBA) was performed. This CBA applied the logic that an increase of DNA profile uploads to a DNA database due to a sheer increase in number of markers and a greater sensitivity of detection afforded with NGS and a higher hit/association rate due to large SNP/kinship resolution and genealogy will increase investigative leads, will be more effective for identifying recidivists which in turn reduces future victims of crime, and will bring greater safety and security to communities. Analyses were performed for worst case/best case scenarios as well as by simulation sampling the range spaces with multiple input values simultaneously to generate best estimate summary statistics. This study shows that the benefits, both tangible and intangible, over the lifetime of an advanced database system would be huge and can be projected to be for less than $1 billion per year (over a 10-year period) investment can reap on average > $4.8 billion in tangible and intangible cost-benefits per year. More importantly, on average > 50,000 individuals need not become victims if FIGG were employed, assuming investigative associations generated were acted upon. The benefit to society is immense making the laboratory investment a nominal cost. The benefits likely are underestimated herein. There is latitude in the estimated costs, and even if they were doubled or tripled, there would still be substantial benefits gained with a FIGG-based approach. While the data used in this CBA are US centric (primarily because data were readily accessible), the model is generalizable and could be used by other jurisdictions to perform relevant and representative CBAs.
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Affiliation(s)
- Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.
- Radford University Forensic Science Institute, Radford University, Radford, VA, USA.
| | - Andrew Arnette
- Department of Business Information Technology, Virginia Tech, Blacksburg, VA, USA
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
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5
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Vinueza-Espinosa DC, Cuesta-Aguirre DR, Malgosa A, Santos C. Mitochondrial DNA control region typing from highly degraded skeletal remains by single-multiplex next-generation sequencing. Electrophoresis 2023; 44:1423-1434. [PMID: 37379235 DOI: 10.1002/elps.202200052] [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: 02/28/2022] [Revised: 03/29/2023] [Accepted: 06/08/2023] [Indexed: 06/30/2023]
Abstract
Poor nuclear DNA preservation from highly degraded skeletal remains is the most limiting factor for the genetic identification of individuals. Mitochondrial DNA (mtDNA) typing, and especially of the control region (CR), using next-generation sequencing (NGS), enables retrieval of valuable genetic information in forensic contexts where highly degraded human skeletal remains are the only source of genetic material. Currently, NGS commercial kits can type all mtDNA-CR in fewer steps than the conventional Sanger technique. The PowerSeq CRM Nested System kit (Promega Corporation) employs a nested multiplex-polymerase chain reaction (PCR) strategy to amplify and index all mtDNA-CR in a single reaction. Our study analyzes the success of mtDNA-CR typing of highly degraded human skeletons using the PowerSeq CRM Nested System kit. We used samples from 41 individuals from different time periods to test three protocols (M1, M2, and M3) based on modifications of PCR conditions. To analyze the detected variants, two bioinformatic procedures were compared: an in-house pipeline and the GeneMarker HTS software. The results showed that many samples were not analyzed when the standard protocol (M1) was used. In contrast, the M3 protocol, which includes 35 PCR cycles and longer denaturation and extension steps, successfully recovered the mtDNA-CR from highly degraded skeletal samples. Mixed base profiles and the percentage of damaged reads were both indicators of possible contamination and can provide better results if used together. Furthermore, our freely available in-house pipeline can provide variants concordant with the forensic software.
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Affiliation(s)
- Diana C Vinueza-Espinosa
- Research Group in Biological Anthropology, Biological Anthropology Unit, Department of Animal Biology, Vegetal Biology and Ecology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Daniel R Cuesta-Aguirre
- Research Group in Biological Anthropology, Biological Anthropology Unit, Department of Animal Biology, Vegetal Biology and Ecology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Assumpció Malgosa
- Research Group in Biological Anthropology, Biological Anthropology Unit, Department of Animal Biology, Vegetal Biology and Ecology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Cristina Santos
- Research Group in Biological Anthropology, Biological Anthropology Unit, Department of Animal Biology, Vegetal Biology and Ecology, Universitat Autònoma de Barcelona, Bellaterra, Spain
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6
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Korber JT, Canale LC, Holland MM. Massively Parallel Sequencing of the Mitogenome from Human Hair Shafts in Forensic Investigations. Curr Protoc 2023; 3:e865. [PMID: 37579069 DOI: 10.1002/cpz1.865] [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] [Indexed: 08/16/2023]
Abstract
This article highlights methods used to perform DNA extraction, mitochondrial DNA quantification, multiplex PCR amplification, amplicon-based massively parallel sequencing, and data analysis of the mitochondrial genome (mitogenome) from human hair shafts. The focus is on applications to forensic casework, but this set of protocols can be used for any purpose involving small cuttings (as small as 1 to 5 mm) of human hair shafts up to 40 years from the time of collection. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Extraction of mitochondrial DNA from human hair shafts Basic Protocol 2: Quantification of mitochondrial DNA (copies/μl) Basic Protocol 3: Multiplex amplification of the mitogenome Basic Protocol 4: Library preparation and sequencing of mitogenome amplicons Basic Protocol 5: Data analysis of mitogenome haplotypes.
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Affiliation(s)
- Jade T Korber
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
| | - Lauren C Canale
- Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
- Mitotyping Technologies, State College, Pennsylvania
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7
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Skonieczna K, Grzybowski T. Capability of the iSeq 100 sequencing system from Illumina to detect low-level substitutions in the human mitochondrial genome. Forensic Sci Int Genet 2023; 66:102912. [PMID: 37451073 DOI: 10.1016/j.fsigen.2023.102912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The significance of mtDNA heteroplasmy in forensic and medical genetics has increased recently because massively parallel sequencing (MPS) technologies enable more accurate and precise detection of minority nucleotide variants. Recent reports have shown that detection of low-level substitutions may depend on library preparation or sequencing protocol, and can vary for different MPS platforms. The MiSeq (Illumina) and Ion S5 (Thermo Fisher Scientific) are mainly used for heteroplasmy detection, but no data are available regarding the iSeq 100, an Illumina platform of the smallest throughput. Notably, unlike the other systems, the machine utilizes sequencing by synthesis one-channel chemistry to determine DNA sequences. Thus, it is important to verify the capability of the iSeq 100 system to determine mitochondrial haplotypes and detect heteroplasmic substitutions. In this study, previously determined entire mitochondrial genomes were sequenced with the iSeq 100 system. Each mitogenome was sequenced twice, giving approximately 2000x and 10,000x coverage. All homoplasmic mutations and minority variants above the 19 % level detected with the iSeq 100 system were also observed after dideoxy sequencing. Moreover, all heteroplasmic substitutions above the 2 % level were consistently detected with SBS one-channel chemistry. However, detection of low-level mtDNA variants may require additional, confirmatory experiments. In summary, the iSeq 100 system enables reproducible and accurate sequencing of human mitochondrial genomes. Detection of mtDNA minority variants depends on the laboratory protocol and sequencing platform used, but homoplasmic mutations and heteroplasmy above the 2 % level can be correctly detected with the iSeq 100 system.
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Affiliation(s)
- Katarzyna Skonieczna
- Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland.
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland
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8
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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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9
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Peng D, Geng J, Yang J, Liu J, Wang N, Wu R, Sun H. Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel. Genes (Basel) 2023; 14:genes14040912. [PMID: 37107670 PMCID: PMC10137955 DOI: 10.3390/genes14040912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is an effective genetic marker in forensic practice, especially for aged bones and hair shafts. Detection of the whole mitochondrial genome (mtGenome) using traditional Sanger-type sequencing is laborious and time-consuming. Additionally, its ability to distinguish point heteroplasmy (PHP) and length heteroplasmy (LHP) is limited. The application of massively parallel sequencing in mtDNA detection helps researchers to study the mtGenome in-depth. The ForenSeq mtDNA Whole Genome Kit, which contains a total of 245 short amplicons, is one of the multiplex library preparation kits for the mtGenome. We used this system to detect the mtGenome in the blood samples and hair shafts of thirty-three individuals from eight two-generation pedigrees, one three-generation pedigree, and one four-generation pedigree. High-quality sequencing results were obtained. Ten unique mtGenome haplotypes were observed in the mothers from the ten pedigrees. A total of 26 PHPs were observed using the interpretation threshold of 6%. Eleven types of LHPs in six regions were evaluated in detail. When considering homoplasmic variants only, consistent mtGenome haplotypes were observed between the twice-sequenced libraries and between the blood and hair shafts from the same individual and among maternal relatives in the pedigrees. Four inherited PHPs were observed, and the remainder were de novo/disappearing PHPs in the pedigrees. Our results demonstrate the effective capability of the ForenSeq mtDNA Whole Genome Kit to generate the complete mtGenome in blood and hair shafts, as well as the complexity of mtDNA haplotype comparisons between different types of maternal relatives when heteroplasmy is considered.
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Affiliation(s)
- Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
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10
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Stephens KM, Barta R, Fleming K, Perez JC, Wu SF, Snedecor J, Holt CL, LaRue B, Budowle B. Developmental validation of the ForenSeq MainstAY kit, MiSeq FGx sequencing system and ForenSeq Universal Analysis Software. Forensic Sci Int Genet 2023; 64:102851. [PMID: 36907074 DOI: 10.1016/j.fsigen.2023.102851] [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: 11/10/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
For human identification purposes, forensic genetics has primarily relied upon a core set of autosomal (and to a lesser extent Y chromosome) short tandem repeat (STR) markers that are enriched by amplification using the polymerase chain reaction (PCR) that are subsequently separated and detected using capillary electrophoresis (CE). While STR typing conducted in this manner is well-developed and robust, advances in molecular biology that have occurred over the last 15 years, in particular massively parallel sequencing (MPS) [1-7], offer certain advantages as compared to CE-based typing. First and foremost is the high throughput capacity of MPS. Current bench top high throughput sequencers enable larger batteries of markers to be multiplexed and multiple samples to be sequenced simultaneously (e.g., millions to billions of nucleotides can be sequenced in one run). Second, compared to the length-based CE approach, sequencing STRs increases discrimination power, enhances sensitivity of detection, reduces noise due to instrumentation, and improves mixture interpretation [4,8-23]. Third, since detection of STRs is based on sequence and not fluorescence, amplicons can be designed that are shorter in length and of similar lengths among loci, where possible, which can improve amplification efficiency and analysis of degraded samples. Lastly, MPS offers a single format approach that can be applied to analysis of a wide variety of genetic markers of forensic interest (e.g., STRs, mitochondrial DNA, single nucleotide polymorphisms, insertion/deletions). These features make MPS a desirable technology for casework [14,15,24,25-48]. The developmental validation of the ForenSeq MainstAY library preparation kit with the MiSeq FGx Sequencing System and ForenSeq Universal Software is reported here to assist with validation of this MPS system for casework [49]. The results show that the system is sensitive, accurate and precise, specific, and performs well with mixtures and mock case-type samples.
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Affiliation(s)
| | - Richelle Barta
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Keenan Fleming
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | | | - Shan-Fu Wu
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - June Snedecor
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Cydne L Holt
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bobby LaRue
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bruce Budowle
- University of Helsinki, Department of Forensic Medicine, Haartmaninkatu 8, P.O. Box 63, Helsinki 00014, Finland
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11
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Foley MM, Oldoni F. A global snapshot of current opinions of next-generation sequencing technologies usage in forensics. Forensic Sci Int Genet 2023; 63:102819. [PMID: 36509023 DOI: 10.1016/j.fsigen.2022.102819] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/28/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
The future of forensic DNA testing is being shaped by the research and usage of next-generation systems, which have increased the multiplexing capabilities of the field and the type and amount of genetic data that can be utilized for investigations. The NGS adoption for casework has been slow, albeit the plethora of data that has been published. This study evaluated the current opinions on sequencing in forensics. A 20-question online-survey focusing on NGS knowledge, training, and usage was distributed to 6001 forensic DNA researchers and practitioners worldwide. A total of 367 responses were obtained from all continents (North/South America (69.8%), Europe (21.2%), Asia (5.5%), Oceania (2.5%), and Africa (1%)). The respondents consisted of 50% practitioners, 31% researchers, and 19% both. Of these, 38% already own a next-gen sequencing instrument, and 13% are planning to purchase one. Overall, there exists an extensive knowledge on next-gen sequencing within the forensic community, including among laboratories that have not yet implemented this high-throughput technology in their workflows. Current usage focuses primarily on SNP analysis for investigative leads and mitochondrial DNA analysis while future applications included both STR and SNP testing applied to general casework. The major overall concerns respondents have for implementing a sequencing instrument include limited funding, staffing, lack of time, and the cost-effectiveness of providing this service. Specific technical concerns that the respondents had are the lack of training, statistical applications, bioinformatics support, and of rigorous guidelines and recommendations. Most of the respondents do believe there will be a technology shift from using CE only to the use of NGS on casework in 5-10 years. In addition, around 66% of respondents believe that it is moderately to very likely that the court will accept sequencing analysis. Sixteen percent fell in the middle, and the remaining 15% believe it is more unlikely, with 3% of respondents believing it is very unlikely. In conclusion, this work outlines current analytical challenges experienced by the global forensic DNA community and addresses different strategies for the implementation of next-gen sequencing technologies in casework.
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Affiliation(s)
- Megan M Foley
- The George Washington University, Department of Forensic Sciences, 2100 Foxhall Rd, Washington, DC 20007, United States
| | - Fabio Oldoni
- Arcadia University, Department of Chemistry & Physics, 450 S Easton Rd, Glenside, PA 19038, United States.
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12
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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13
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Development and validation of a SYBR green-based mitochondrial DNA quantification method by following the MIQE and other guidelines. Leg Med (Tokyo) 2022; 58:102096. [PMID: 35689884 DOI: 10.1016/j.legalmed.2022.102096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 01/28/2023]
Abstract
In forensic mitochondrial DNA (mtDNA) analysis, quantitative PCR (qPCR) is usually performed to obtain high-quality sequence data for subsequent Sanger or massively parallel sequencing. Unlike methods for nuclear DNA quantification using qPCR, a calibrator is necessary to obtain mtDNA concentrations (i.e., copies/µL). Herein, we developed and validated a mtDNA quantification method based on a SYBR Green assay by following MIQE [Bustin et al., Clin. Chem. 55 (2009) 611-22] and other guidelines. Primers were designed to amplify nucleotide positions 16,190-16,420 in hypervariable region 1 for qPCR using PowerUp SYBR Green and QuantStudio 5. The optimized conditions were 0.3 µM each primer and an annealing temperature of 60 °C under a 2-step cycling protocol. K562 DNA at 100 pg/µL was converted into a mtDNA concentration of 16,400 copies/µL using linearized plasmid DNA. This mtDNA calibrator was obtained by cloning the synthesized DNA fragments of mtDNA (positions 16,140-16,470) containing a 100-bp inversion. The linear dynamic range of the K562 standard curve was 10,000-0.1 pg/µL (r2 ≥ 0.999). The accuracy was examined using NIST SRM 2372a, and its components A, B, and C were quantified with differences of -29.4%, -35.0%, and -22.0%, respectively, against the mtDNA concentrations calculated from published NIST data. We also examined the specificity of the primers, stability of the reaction mix, precision, tolerance against PCR inhibitors, and cross-reactivity against DNA from various animal taxa. Our newly developed mtDNA quantification method is expected to be useful for forensic mtDNA analysis.
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14
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Gutierrez R, Roman MG, Harrel M, Hughes S, LaRue B, Houston R. Assessment of the ForenSeq mtDNA control region kit and comparison of orthogonal technologies. Forensic Sci Int Genet 2022; 59:102721. [DOI: 10.1016/j.fsigen.2022.102721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/13/2022] [Accepted: 05/08/2022] [Indexed: 11/04/2022]
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15
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McElhoe JA, Wilton PR, Parson W, Holland MM. Exploring statistical weight estimates for mitochondrial DNA matches involving heteroplasmy. Int J Legal Med 2022; 136:671-685. [PMID: 35243529 DOI: 10.1007/s00414-022-02774-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows forensic laboratories to report heteroplasmy on a routine basis. Statistical approaches will be needed to determine the relative frequency of observing an mtDNA haplotype when including the presence of a heteroplasmic site. Here, we examined 1301 control region (CR) sequences, collected from individuals in four major population groups (European, African, Asian, and Latino), and covering 24 geographically distributed haplogroups, to assess the rates of point heteroplasmy (PHP) on an individual and nucleotide position (np) basis. With a minor allele frequency (MAF) threshold of 2%, the data was similar across population groups, with an overall PHP rate of 37.7%, and the majority of heteroplasmic individuals (77.3%) having only one site of heteroplasmy. The majority (75.2%) of identified PHPs had an MAF of 2-10%, and were observed at 12.6% of the nps across the CR. Both the broad and phylogenetic testing suggested that in many cases the low number of observations of heteroplasmy at any one np results in a lack of statistical association. The posterior frequency estimates, which skew conservative to a degree depending on the sample size in a given haplogroup, had a mean of 0.152 (SD 0.134) and ranged from 0.031 to 0.83. As expected, posterior frequency estimates decreased in accordance with 1/n as the sample size (n) increased. This provides a proposed conservative statistical framework for assessing haplotype/heteroplasmy matches when applying an MPS technique in forensic cases and will allow for continual refinement as more data is generated, both within the CR and across the mitochondrial genome.
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Affiliation(s)
- Jennifer A McElhoe
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA.
| | - Peter R Wilton
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- 23andMe Inc, Sunnyvale, CA, 94086, USA
| | - Walther Parson
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
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16
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Nakanishi H, Yoneyama K, Hara M, Takada A, Sakai K, Saito K. Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq. Int J Legal Med 2022; 136:423-432. [PMID: 35001166 DOI: 10.1007/s00414-021-02763-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022]
Abstract
We tried to estimate individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq. The BAM files produced by MiSeq were viewed using Integrative Genomics Viewer (IGV) to verify mixed bases. By sorting the reads according to base type for each mixed base, partial haplotypes were determined. Then, the BAM files produced by MinKNOW were viewed using IGV. To determine haplotypes with IGV, only mixed bases determined by MiSeq were used as target bases. By sorting the reads according to base type for each target base, each contributor's haplotype was estimated. In mixed samples from two contributors, even a haplotype with a minor contribution of 5% could be distinguished from the haplotype of the major contributor. In mixed samples of three contributors (mixture ratios of 1:1:1 and 4:2:1), each haplotype could also be distinguished. Sequences of C-stretches were determined very inaccurately in the MinION analysis. Although the analysis method was simple, each haplotype was correctly detected in all mixed samples with two or three contributors in various mixture ratios by combining MinION and MiSeq. This should be useful for identifying contributors to mixed samples.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
| | - Katsumi Yoneyama
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Masaaki Hara
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Kentaro Sakai
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo, 112-0012, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
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17
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Cortes-Figueiredo F, Carvalho FS, Fonseca AC, Paul F, Ferro JM, Schönherr S, Weissensteiner H, Morais VA. From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. Int J Mol Sci 2021; 22:12031. [PMID: 34769461 PMCID: PMC8584537 DOI: 10.3390/ijms222112031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 02/06/2023] Open
Abstract
Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS's variants (TSS found 57.92% of PCP's variants), with a significant correlation between the variant levels of variants found with both pipelines.
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Affiliation(s)
- Filipe Cortes-Figueiredo
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Filipa S. Carvalho
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
| | - Ana Catarina Fonseca
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Friedemann Paul
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - José M. Ferro
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Vanessa A. Morais
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
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18
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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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Faccinetto C, Sabbatini D, Serventi P, Rigato M, Salvoro C, Casamassima G, Margiotta G, De Fanti S, Sarno S, Staiti N, Luiselli D, Marino A, Vazza G. Internal validation and improvement of mitochondrial genome sequencing using the Precision ID mtDNA Whole Genome Panel. Int J Legal Med 2021; 135:2295-2306. [PMID: 34491421 PMCID: PMC8523450 DOI: 10.1007/s00414-021-02686-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/13/2021] [Indexed: 12/26/2022]
Abstract
With the recent advances in next-generation sequencing (NGS), mitochondrial whole-genome sequencing has begun to be applied to the field of the forensic biology as an alternative to the traditional Sanger-type sequencing (STS). However, experimental workflows, commercial solutions, and output data analysis must be strictly validated before being implemented into the forensic laboratory. In this study, we performed an internal validation for an NGS-based typing of the entire mitochondrial genome using the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific) on the Ion S5 sequencer (Thermo Fisher Scientific). Concordance, repeatability, reproducibility, sensitivity, and heteroplasmy detection analyses were assessed using the 2800 M and 9947A standard control DNA as well as typical casework specimens, and results were compared with conventional Sanger sequencing and another NGS sequencer in a different laboratory. We discuss the strengths and limitations of this approach, highlighting some issues regarding noise thresholds and heteroplasmy detection, and suggesting solutions to mitigate these effects and improve overall data interpretation. Results confirmed that the Precision ID Whole mtDNA Genome Panel is highly reproducible and sensitive, yielding useful full mitochondrial DNA sequences also from challenging DNA specimens, thus providing further support for its use in forensic practice.
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Affiliation(s)
- Christian Faccinetto
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy.
| | - Daniele Sabbatini
- Department of Neurosciences DNS, University of Padova, Padova, Italy
| | - Patrizia Serventi
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Martina Rigato
- Department of Biology, University of Padova, Padova, Italy
| | | | - Gianluca Casamassima
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Gianluca Margiotta
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Sara De Fanti
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre Alma Mater Research Institute On Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
| | - Stefania Sarno
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Nicola Staiti
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alberto Marino
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Giovanni Vazza
- Department of Biology, University of Padova, Padova, Italy.
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20
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Mandape SN, Smart U, King JL, Muenzler M, Kapema KB, Budowle B, Woerner AE. MMDIT: A tool for the deconvolution and interpretation of mitochondrial DNA mixtures. Forensic Sci Int Genet 2021; 55:102568. [PMID: 34416654 DOI: 10.1016/j.fsigen.2021.102568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/22/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023]
Abstract
Short tandem repeats of the nuclear genome have been the preferred markers for analyzing forensic DNA mixtures. However, when nuclear DNA in a sample is degraded or limited, mitochondrial DNA (mtDNA) markers provide a powerful alternative. Though historically considered challenging, the interpretation and analysis of mtDNA mixtures have recently seen renewed interest with the advent of massively parallel sequencing. However, there are only a few software tools available for mtDNA mixture interpretation. To address this gap, the Mitochondrial Mixture Deconvolution and Interpretation Tool (MMDIT) was developed. MMDIT is an interactive application complete with a graphical user interface that allows users to deconvolve mtDNA (whole or partial genomes) mixtures into constituent donor haplotypes and estimate random match probabilities on these resultant haplotypes. In cases where deconvolution might not be feasible, the software allows mixture analysis directly within a binary framework (i.e. qualitatively, only using data on allele presence/absence). This paper explains the functionality of MMDIT, using an example of an in vitro two-person mtDNA mixture with a ratio of 1:4. The uniqueness of MMDIT lies in its ability to resolve mixtures into complete donor haplotypes using a statistical phasing framework before mixture analysis and evaluating statistical weights employing a novel graph algorithm approach. MMDIT is the first available open-source software that can automate mtDNA mixture deconvolution and analysis. The MMDIT web application can be accessed online at https://www.unthsc.edu/mmdit/. The source code is available at https://github.com/SammedMandape/MMDIT_UI and archived on zenodo (https://doi.org/10.5281/zenodo.4770184).
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Affiliation(s)
- Sammed N Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Kapema Bupe Kapema
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
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21
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Ta MTA, Nguyen NN, Tran DM, Nguyen TH, Vu TA, Le DT, Le PT, Do TTH, Hoang H, Chu HH. Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system. Int J Legal Med 2021; 135:2285-2294. [PMID: 34196785 DOI: 10.1007/s00414-021-02649-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
Mitochondrial DNA (mtDNA) analysis using Sanger sequencing has been a routine practice for the identification of human skeletal remains. However, this process is usually challenging since DNA from the remains is highly degraded and at low concentration. Recently, the advent and implementation of massively parallel sequencing (MPS) have been offered the ability to improve mtDNA sequence data for forensic analysis. To assess the utility of the Ion S5™ system - an MPS platform for mtDNA analysis in challenging samples, we sequenced the mitochondrial control region of 52 age-old skeletal remains. Using the Precision ID mtDNA Control Region Panel, 50 full and two partial control region haplotypes at relatively high mean coverage of 2494 × were achieved for variant calling. Further variant analysis at 10% threshold for point heteroplasmy showed high degradation degree in terms of DNA damage in our bone samples. A higher point heteroplasmy threshold of 20% was required to diminish most of background noise caused by the damage. The results from this study indicated the potential application of the Ion S5™ system in sequencing degraded samples in Vietnam and provided valuable data sources for forensic analyses in the future.
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Affiliation(s)
- May Thi Anh Ta
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nam Ngoc Nguyen
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Duc Minh Tran
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trang Hong Nguyen
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Tuan Anh Vu
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dung Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phuong Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thu Thi Hong Do
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Hoang Ha Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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22
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Smart U, Cihlar JC, Budowle B. International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions. Forensic Sci Int Genet 2021; 54:102551. [PMID: 34134047 DOI: 10.1016/j.fsigen.2021.102551] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu SF. Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software. Genes (Basel) 2021; 12:genes12040599. [PMID: 33921728 PMCID: PMC8073089 DOI: 10.3390/genes12040599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
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Vasiljevic N, Lim M, Humble E, Seah A, Kratzer A, Morf NV, Prost S, Ogden R. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Sci Int Genet 2021; 53:102493. [PMID: 33770699 DOI: 10.1016/j.fsigen.2021.102493] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/09/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022]
Abstract
Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.
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Affiliation(s)
- Nina Vasiljevic
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Marisa Lim
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK
| | - Adeline Seah
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Adelgunde Kratzer
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Nadja V Morf
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany; South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK; TRACE Wildlife Forensics Network, Edinburgh, UK
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An alternate workflow for preparing Precision ID Ancestry and Identity Panel libraries for Illumina sequencing. Int J Legal Med 2021; 135:1717-1726. [PMID: 33665703 DOI: 10.1007/s00414-021-02549-4] [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: 11/03/2020] [Accepted: 02/18/2021] [Indexed: 10/22/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are well-established for forensic applications. Although they are not compatible with existing criminal databases, they offer some advantages over short tandem repeat (STR) markers including smaller amplicons, no stutter artifacts, and biogeographic ancestry and phenotype predictions. The Precision ID NGS System, a commercial workflow by Thermo Fisher Scientific, offers a streamlined solution for genotyping forensically relevant SNPs using next-generation sequencing. The Precision ID Ancestry and Identity Panels combined target 289 SNPs, and their sensitivity, reproducibility, and accuracy have been evaluated by the forensic community. The aim of this study was to develop an alternative workflow to genotype these SNP panels using Illumina chemistry. Commercial genomic DNAs (gDNAs) (n, 3) were amplified using three uracil-tolerant polymerase master mixes. Resulting amplicons were prepared into libraries using the KAPA Hyper Prep Kit (KAPA Biosystems) and sequenced via Illumina's MiniSeq. Reads were analyzed using a published analysis pipeline to compile final genotypes with read depth information. Phusion U Multiplex PCR Master Mix (Thermo Fisher Scientific) statistically outperformed the other master mixes tested (P <0.0001), with respect to the number of SNPs genotyped. To ensure a workflow using Phusion U would be compatible across diverse samples, we optimized PCR cycle number using the same commercial gDNAs (n, 3), reference buccal swabs (n, 3), and environmental (household dust) samples (n, 6). Using the developed workflow, 93.9% of all SNPs were successfully genotyped across sample types. Implementation of the developed workflow should be straightforward for forensic laboratories and suitable for processing reference and casework samples.
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Weissensteiner H, Forer L, Fendt L, Kheirkhah A, Salas A, Kronenberg F, Schoenherr S. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res 2021; 31:309-316. [PMID: 33452015 PMCID: PMC7849411 DOI: 10.1101/gr.256545.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/30/2020] [Indexed: 01/14/2023]
Abstract
Within-species contamination is a major issue in sequencing studies, especially for mitochondrial studies. Contamination can be detected by analyzing the nuclear genome or by inspecting polymorphic sites in the mitochondrial genome (mtDNA). Existing methods using the nuclear genome are computationally expensive, and no appropriate tool for detecting sample contamination in large-scale mtDNA data sets is available. Here we present haplocheck, a tool that requires only the mtDNA to detect contamination in both targeted mitochondrial and whole-genome sequencing studies. Our in silico simulations and amplicon mixture experiments indicate that haplocheck detects mtDNA contamination accurately and is independent of the phylogenetic distance within a sample mixture. By applying haplocheck to The 1000 Genomes Project Consortium data, we further evaluate the application of haplocheck as a fast proxy tool for nDNA-based contamination detection using the mtDNA and identify the mitochondrial copy number within a mixture as a critical component for the overall accuracy. The haplocheck tool is available both as a command-line tool and as a cloud web service producing interactive reports that facilitates the navigation through the phylogeny of contaminated samples.
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Affiliation(s)
- Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Liane Fendt
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Azin Kheirkhah
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15782, Galicia, Spain
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
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Assessment of Illumina® Human mtDNA Genome assay: workflow evaluation with development of analysis and interpretation guidelines. Int J Legal Med 2021; 135:1161-1178. [PMID: 33511452 DOI: 10.1007/s00414-021-02508-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/08/2021] [Indexed: 01/27/2023]
Abstract
Mitochondrial DNA (mtDNA) is a small but significant part of the human genome, whose applicability potential has gradually increased with the advent of massively parallel sequencing (MPS) technology. Knowledge of the particular workflow, equipment, and reagents used, along with extensive usage of negative controls to monitor all preparation steps constitute the prerequisites for confident reporting of results. In this study, we performed an assessment of Illumina® Human mtDNA Genome assay on MiSeq FGx™ instrument. Through analysis of several types of negative controls, as well as mtDNA positive controls, we established thresholds for data analysis and interpretation, consisting of several components: minimum read depth (220 reads), minimum quality score (41), percentage of minor allele sufficient for analysis (3.0%), percentage of minor allele sufficient for interpretation (6.0%), and percentage of major allele sufficient for homoplasmic variant call (97.0%). Based on these criteria, we defined internal guidelines for analysis and interpretation of mtDNA results obtained by MPS. Our study shows that the whole mtDNA assay on MiSeq FGx™ produces repeatable and reproducible results, independent of the analyst, which are also concordant with Sanger-type sequencing results for mtDNA control region, as well as with MPS results produced by NextSeq®. Overall, established thresholds and interpretation guidelines were successfully applied for the sequencing of complete mitochondrial genomes from high-quality samples. The underlying principles and proposed methodology on the definition of internal laboratory guidelines for analysis and interpretation of MPS results may be applicable to similar MPS workflows, e.g. targeting good-quality samples in forensic genetics and molecular diagnostics.
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Crysup B, Woerner AE, King JL, Budowle B. Graph Algorithms for Mixture Interpretation. Genes (Basel) 2021; 12:genes12020185. [PMID: 33514030 PMCID: PMC7911948 DOI: 10.3390/genes12020185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/19/2022] Open
Abstract
The scale of genetic methods are presently being expanded: forensic genetic assays previously were limited to tens of loci, but now technologies allow for a transition to forensic genomic approaches that assess thousands to millions of loci. However, there are subtle distinctions between genetic assays and their genomic counterparts (especially in the context of forensics). For instance, forensic genetic approaches tend to describe a locus as a haplotype, be it a microhaplotype or a short tandem repeat with its accompanying flanking information. In contrast, genomic assays tend to provide not haplotypes but sequence variants or differences, variants which in turn describe how the alleles apparently differ from the reference sequence. By the given construction, mitochondrial genetic assays can be thought of as genomic as they often describe genetic differences in a similar way. The mitochondrial genetics literature makes clear that sequence differences, unlike the haplotypes they encode, are not comparable to each other. Different alignment algorithms and different variant calling conventions may cause the same haplotype to be encoded in multiple ways. This ambiguity can affect evidence and reference profile comparisons as well as how “match” statistics are computed. In this study, a graph algorithm is described (and implemented in the MMDIT (Mitochondrial Mixture Database and Interpretation Tool) R package) that permits the assessment of forensic match statistics on mitochondrial DNA mixtures in a way that is invariant to both the variant calling conventions followed and the alignment parameters considered. The algorithm described, given a few modest constraints, can be used to compute the “random man not excluded” statistic or the likelihood ratio. The performance of the approach is assessed in in silico mitochondrial DNA mixtures.
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Affiliation(s)
- Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; (A.E.W.); (J.L.K.); (B.B.)
- Correspondence:
| | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; (A.E.W.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; (A.E.W.); (J.L.K.); (B.B.)
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; (A.E.W.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Smart U, Cihlar JC, Mandape SN, Muenzler M, King JL, Budowle B, Woerner AE. A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures. Genes (Basel) 2021; 12:128. [PMID: 33498312 PMCID: PMC7909279 DOI: 10.3390/genes12020128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment of external reference panels containing information on haplotypic variation (from similar and different haplogroups) was leveraged to assess the effect of panel composition on phasing accuracy. Building on these simulations, mitochondrial genomes from the Human Mitochondrial DataBase were sourced to populate the panels and key parameter values were identified by deconvolving an additional 7290 in silico two-person mixtures. Finally, employing an optimized reference panel and phasing parameters, the approach was validated with in vitro two-person mixtures with differing proportions. Deconvolution was most accurate when the haplotypes in the mixture were similar to haplotypes present in the reference panel and when the mixture ratios were neither highly imbalanced nor subequal (e.g., 4:1). Overall, errors in haplotype estimation were largely bounded by the accuracy of the mixture's genotype results. The proposed framework is the first available approach that automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Sammed N. Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Grabell S, Shomron N. DNA Data Collection and Analysis in the Forensic Arena. Methods Mol Biol 2021; 2243:355-368. [PMID: 33606268 DOI: 10.1007/978-1-0716-1103-6_19] [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] [Indexed: 06/12/2023]
Abstract
Recent scientific advancements in the field of genetics have fostered significant changes for the criminal justice system. Growing National DNA databases, public DNA databases, private direct-to-consumer (DTC) DNA testing companies, and improvements in next-generation sequencing (NGS) have resulted in effective methods for tracking down criminals and exonerating the innocent. While these recently discovered and profound techniques seem to provide benefits, their use in forensic detection has become subject to harsh legal opposition. Ultimately, should law enforcement be permitted to analyze DNA found at crime scenes and DNA that has accumulated in national, public, and private databases to aid in their investigations, or are individuals' privacy rights breached in the process?
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Affiliation(s)
- Sydnie Grabell
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Mita Y, Fukagawa T, Watahiki H, Kitayama T, Fujii K, Mizuno N, Sekiguchi K. Developmental validation for Sanger sequencing of HV1 and HV2 in mitochondrial DNA. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2020. [DOI: 10.1016/j.fsir.2020.100159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Cihlar JC, Amory C, Lagacé R, Roth C, Parson W, Budowle B. Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel. Genes (Basel) 2020; 11:E1345. [PMID: 33202822 PMCID: PMC7709034 DOI: 10.3390/genes11111345] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology-Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge-has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly accurate and reproducible results were generated for a variety of sample qualities and quantities, supporting the reliability of this specific whole genome mitochondrial DNA MPS system for analysis of forensic biological evidence.
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Affiliation(s)
- Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA;
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.A.); (W.P.)
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA; (R.L.); (C.R.)
| | - Chantal Roth
- Human Identification Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA; (R.L.); (C.R.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.A.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA;
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
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Mitochondrial Sequencing of Missing Persons DNA Casework by Implementing Thermo Fisher's Precision ID mtDNA Whole Genome Assay. Genes (Basel) 2020; 11:genes11111303. [PMID: 33158032 PMCID: PMC7692767 DOI: 10.3390/genes11111303] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
The advent of massively parallel sequencing (MPS) in the past decade has opened the doors to mitochondrial whole-genome sequencing. Mitochondrial (mt) DNA is used in forensics due to its high copy number per cell and maternal mode of inheritance. Consequently, we have implemented the Thermo Fisher Precision ID mtDNA Whole Genome panel coupled with the Ion Chef™ and Ion S5™ for MPS analysis in the California Department of Justice, Missing Persons DNA Program. Thirty-one mostly challenging samples (degraded, inhibited, low template, or mixed) were evaluated for this study. The majority of these samples generated single source full or partial genome sequences with MPS, providing information in cases where previously there was none. The quantitative and sensitive nature of MPS analysis was beneficial, but also led to detection of low-level contaminants. In addition, we found Precision ID to be more susceptible to inhibition than our legacy Sanger assay. Overall, the success rate (full single source hypervariable regions I and II (HVI/HVII) for Sanger and control region for MPS result) for these challenging samples increased from 32.3% with Sanger sequencing to 74.2% with the Precision ID assay. Considering the increase in success rate, the simple workflow and the higher discriminating potential of whole genome data, the Precision ID platform is a significant improvement for the CA Department of Justice Missing Persons DNA Program.
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Distinguishing mitochondrial DNA and NUMT sequences amplified with the precision ID mtDNA whole genome panel. Mitochondrion 2020; 55:122-133. [PMID: 32949792 DOI: 10.1016/j.mito.2020.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 11/22/2022]
Abstract
Nuclear mitochondrial DNA segments (NUMTs) are generated via transfer of portions of the mitochondrial genome into the nuclear genome. Given their common origin, there is the possibility that both the mitochondrial and NUMT segments may co-amplify using the same set of primers. Thus, analysis of the variation of the mitochondrial genome must take into account this co-amplification of mitochondrial and NUMT sequences. The study herein builds on data from the study by Strobl et al. (Strobl et al., 2019), in which multiple point heteroplasmies were called with an "N" to prevent labeling NUMT sequences mimicking mitochondrial heteroplasmy and being interpreted as true mitochondrial in origin sequence variants. Each of these point heteroplasmies was studied in greater detail, both molecularly and bioinformatically, to determine whether NUMT or true mitochondrial DNA variation was present. The bioinformatic and molecular tools available to help distinguish between NUMT and mitochondrial DNA and the effect of NUMT sequences on interpretation were discussed.
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35
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England R, Nancollis G, Stacey J, Sarman A, Min J, Harbison S. Compatibility of the ForenSeq™ DNA Signature Prep Kit with laser microdissected cells: An exploration of issues that arise with samples containing low cell numbers. Forensic Sci Int Genet 2020; 47:102278. [DOI: 10.1016/j.fsigen.2020.102278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/05/2020] [Accepted: 03/15/2020] [Indexed: 12/27/2022]
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Delest A, Godfrin D, Chantrel Y, Ulus A, Vannier J, Faivre M, Hollard C, Laurent FX. Sequenced-based French population data from 169 unrelated individuals with Verogen's ForenSeq DNA signature prep kit. Forensic Sci Int Genet 2020; 47:102304. [PMID: 32417726 DOI: 10.1016/j.fsigen.2020.102304] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022]
Abstract
Massively Parallel Sequencing (MPS) applied to forensic genetics allows the simultaneous analysis of hundreds of genetic markers and the access to full amplicon sequences which help to increase available allele diversity. Meanwhile, sequence variation within the repeat regions represents the majority of the allele diversity, flanking regions adjacent to the repeat core provide an additional degree of variation. The forensic genetics community needs access to population data, from relevant parts of the world that contain this new sequence diversity in order to perform statistical calculations. In this study, we report sequence-based Short Tandem Repeat (STR) and identity Single Nucleotide Polymorphism (iSNPs) allele data for 169 French individuals across 58 STRs and 92 SNPs included in the Verogen ForenSeq DNA Signature Prep kit. 42 STRs out of 58 showed an increased number of alleles due to sequence variation in the repeat motif and/or the flanking regions. D9S1122 showed the largest overall gain with an increase of observed heterozygosities of almost 25 %. The combined match probability combining 27 autosomal STRs and 91 identity SNPs was 1.11E-69. Sequence-based allele frequencies included in this publication will help forensic laboratories to increase the power of discrimination for identification, kinship analysis and mixture interpretation.
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Affiliation(s)
- Anna Delest
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France.
| | - Dominique Godfrin
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Yann Chantrel
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Ayhan Ulus
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Julien Vannier
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Magalie Faivre
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Clémence Hollard
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - François-Xavier Laurent
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France.
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Cihlar JC, Peters D, Strobl C, Parson W, Budowle B. The lot-to-lot variability in the mitochondrial genome of controls. Forensic Sci Int Genet 2020; 47:102298. [PMID: 32464353 DOI: 10.1016/j.fsigen.2020.102298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/28/2022]
Abstract
Current research in the biomedical field has illustrated how cell lines used as reference standards can change over time and, more importantly, can affect research and diagnostic results obtained from these cell lines. With the use of increasingly sensitive and highly resolving technologies (e.g., massively parallel sequencing), forensic scientists must be aware of and account for potential variability in the cell lines used as controls in their validation studies and day-to-day casework. In this study, multiple lot numbers from four commonly-used control cell line DNAs were sequenced with massively parallel sequencing on the Ion S5. The variability among these different lots was evaluated, and the effect on forensic laboratory work discussed.
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Affiliation(s)
- Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA.
| | - Dixie Peters
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
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