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Agudo MM, Fantinato C, Roseth A, Aanes H, Gill P, Fonneløp AE, Bleka Ø. A comparison of likelihood ratios calculated from surface DNA mixtures using MPS and CE Technologies. Forensic Sci Int Genet 2024; 73:103111. [PMID: 39128429 DOI: 10.1016/j.fsigen.2024.103111] [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: 01/18/2024] [Revised: 06/14/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024]
Abstract
This study evaluates the performance of analysing surface DNA samples using massively parallel sequencing (MPS) compared to traditional capillary electrophoresis (CE). A total of 30 samples were collected from various surfaces in an office environment and were analysed with CE and MPS. These were compared against 60 reference samples (office inhabitants). To identify contributors, likelihood ratios (LRs) were calculated for MPS and CE data using the probabilistic genotyping software MPSproto and EuroForMix respectively. Although a higher number of sequences/peaks were observed per DNA profile in MPS compared to CE, LR values were found to be lower for MPS data formats. This might be the result of the increased complexity of MPS data, along with a possible elevation of unknown alleles and/or artefacts. The study highlights avenues for improving MPS data quality and analysis to facilitate more robust interpretation of challenging casework-like samples.
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Affiliation(s)
- Maria Martin Agudo
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Chiara Fantinato
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Arne Roseth
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Håvard Aanes
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Peter Gill
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Øyvind Bleka
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway.
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2
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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3
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Zhang J, Liu W, Simayijiang H, Hu P, Yan J. Application of Microbiome in Forensics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00096-1. [PMID: 36031058 PMCID: PMC10372919 DOI: 10.1016/j.gpb.2022.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/29/2022] [Indexed: 06/04/2023]
Abstract
Recent advances in next-generation sequencing technology and improvements in bioinformatics have expanded the scope of microbiome analysis as a forensic tool. Microbiome research is concerned with the study of the compositional profile and diversity of microbial flora as well as the interactions between microbes, hosts, and the environment. It has opened up many new possibilities for forensic analysis. In this review, we discuss various applications of microbiomes in forensics, including identification of individuals, geolocation inference, post-mortem interval (PMI) estimation, and others.
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Affiliation(s)
- Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Wenli Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | | | - Ping Hu
- Key Laboratory of Environment and Health (HUST), Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
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4
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A New String Edit Distance and Applications. ALGORITHMS 2022. [DOI: 10.3390/a15070242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only single-character edits. In forensic applications polymorphic genetic markers such as short tandem repeats (STRs) are used. At these repetitive motifs the DNA copying errors consist of more than just single base differences. More often the phenomenon of “stutter” is observed, where the number of repeated units differs (by whole units) from the template. To adapt the Levenshtein distance to be suitable for forensic applications where DNA sequence similarity is of interest, a generalized string edit distance is defined that accommodates the addition or deletion of whole motifs in addition to single-nucleotide edits. A dynamic programming implementation is developed for computing this distance between sequences. The novelty of this algorithm is in handling the complex interactions that arise between multiple- and single-character edits. Forensic examples illustrate the purpose and use of the Restricted Forensic Levenshtein (RFL) distance measure, but applications extend to sequence alignment and string similarity in other biological areas, as well as dynamic programming algorithms more broadly.
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5
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Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures. Forensic Sci Int Genet 2022; 59:102705. [DOI: 10.1016/j.fsigen.2022.102705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 03/10/2022] [Accepted: 04/10/2022] [Indexed: 12/13/2022]
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6
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Roman MG, Gutierrez R, Houston R. Massively parallel sequencing of Cannabis sativa chloroplast hotspots for forensic typing. J Cannabis Res 2022; 4:13. [PMID: 35300721 PMCID: PMC8928601 DOI: 10.1186/s42238-022-00123-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Marijuana (Cannabis sativa) is the most commonly used illicit drug in the USA, and the use of DNA barcodes could assist drug trafficking investigations by indicating the biogeographical origin and crop type of a sample and providing a means for linking cases. Additionally, the legality of marijuana in the USA remains complicated with some states fully legalizing marijuana for recreational use while federally marijuana remains completely illegal. Massively parallel sequencing (MPS) offers distinct advantages over capillary electrophoresis (CE), including more comprehensive coverage of target loci, analysis of hundreds of markers simultaneously, and high throughput capabilities. METHODS This study reports on the development of a MiSeq FGx® assay targeting seven "hotspot" regions in the Cannabis sativa chloroplast genome that are highly polymorphic and informative in attempts to determine biogeographical origin and distinguishing between marijuana and hemp. Sequencing results were compared to previous studies that used CE-based genotyping methods. RESULTS A total of 49 polymorphisms were observed, 16 of which have not been previously reported. Additionally, sequence data revealed isoalleles at one locus, which were able to differentiate two samples that had the same haplotype using CE-based methods. This study reports preliminary results from sequencing 14 hemp and marijuana samples from different countries using the developed MPS assay. CONCLUSION Future studies should genotype a more comprehensive sample set from around the world to build a haplotype database, which could be used to provide investigative leads for law enforcement agencies investigating marijuana trafficking.
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Affiliation(s)
- Madeline G Roman
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA
| | - Ryan Gutierrez
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA
| | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA.
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7
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DNA typing from skeletal remains: a comparison between capillary electrophoresis and massively parallel sequencing platforms. Int J Legal Med 2020; 134:2029-2035. [DOI: 10.1007/s00414-020-02327-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
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8
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Liu Y, Jin X, Mei S, Lan Q, Fang Y, Liu C, Zhu B. A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies. Electrophoresis 2020; 41:2036-2046. [DOI: 10.1002/elps.202000128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/10/2020] [Accepted: 08/23/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Yanfang Liu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- College of Forensic Medicine Xi'an Jiaotong University Health Science Center Shaanxi P. R. China
| | - Shuyan Mei
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Qiong Lan
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Yating Fang
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Chao Liu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Bofeng Zhu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
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Tozzo P, D’Angiolella G, Brun P, Castagliuolo I, Gino S, Caenazzo L. Skin Microbiome Analysis for Forensic Human Identification: What Do We Know So Far? Microorganisms 2020; 8:microorganisms8060873. [PMID: 32527009 PMCID: PMC7356928 DOI: 10.3390/microorganisms8060873] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 01/15/2023] Open
Abstract
Microbiome research is a highly transdisciplinary field with a wide range of applications and methods for studying it, involving different computational approaches and models. The fact that different people host radically different microbiota highlights forensic perspectives in understanding what leads to this variation and what regulates it, in order to effectively use microbes as forensic evidence. This narrative review provides an overview of some of the main scientific works so far produced, focusing on the potentiality of using skin microbiome profiling for human identification in forensics. This review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The examined literature clearly ascertains that skin microbial communities, although personalized, vary systematically across body sites and time, with intrapersonal differences over time smaller than interpersonal ones, showing such a high degree of spatial and temporal variability that the degree and nature of this variability can constitute in itself an important parameter useful in distinguishing individuals from one another. Even making the effort to organically synthesize all results achieved until now, it is quite evident that these results are still the pieces of a puzzle, which is not yet complete.
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Affiliation(s)
- Pamela Tozzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy;
- Correspondence: ; Tel.: +39-0498272234
| | - Gabriella D’Angiolella
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35121 Padova, Italy;
| | - Paola Brun
- Department of Molecular Medicine, Section of Microbiology, University of Padova, 35121 Padova, Italy; (P.B.); (I.C.)
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, Section of Microbiology, University of Padova, 35121 Padova, Italy; (P.B.); (I.C.)
| | - Sarah Gino
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy;
| | - Luciana Caenazzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy;
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10
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Donaldson ME, Jackson K, Rico Y, Sayers JB, Ethier DM, Kyle CJ. Development of a massively parallel, genotyping-by-sequencing assay in American badger (Taxidea taxus) highlights the need for careful validation when working with low template DNA. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01146-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Education and training in microbial forensics. MICROBIAL FORENSICS 2020. [PMCID: PMC7153755 DOI: 10.1016/b978-0-12-815379-6.00032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Iacobuzio-Donahue CA, Michael C, Baez P, Kappagantula R, Hooper JE, Hollman TJ. Cancer biology as revealed by the research autopsy. Nat Rev Cancer 2019; 19:686-697. [PMID: 31519982 PMCID: PMC7453489 DOI: 10.1038/s41568-019-0199-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/19/2022]
Abstract
A research autopsy is a post-mortem medical procedure performed on a deceased individual with the primary goal of collecting tissue to support basic and translational research. This approach has increasingly been used to investigate the pathophysiological mechanisms of cancer evolution, metastasis and treatment resistance. In this Review, we discuss the rationale for the use of research autopsies in cancer research and provide an evidence-based discussion of the quality of post-mortem tissues compared with other types of biospecimens. We also discuss the advantages of using post-mortem tissues over other types of biospecimens, including the large amounts of tissue that can be obtained and the extent of multiregion sampling that is achievable, which is not otherwise possible in living patients. We highlight how the research autopsy has supported the identification of the clonal origins and modes of spread among metastases, the extent that selective pressures imposed by treatments cause bottlenecks leading to parallel and convergent tumour evolution, and the creation of rare tissue banks and patient-derived model systems. Finally, we comment on the future of the research autopsy as an integral component of precision medicine strategies.
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Affiliation(s)
- Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Chelsea Michael
- Department of Health Informatics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Priscilla Baez
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rajya Kappagantula
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jody E Hooper
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Travis J Hollman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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13
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Nogel M, Pádár Z, Czebe A, Kovács G. Legislation of forensic DNA analysis in Hungary - past, present and future. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Al-Dosari WR, Al-Binali IA, Pydi SS, Goodwin W. Analysis of forensic casework samples by Precision ID Ancestry panel – manual and automated Ampliseq workflow. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
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16
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Bruijns B, Tiggelaar R, Gardeniers H. Massively parallel sequencing techniques for forensics: A review. Electrophoresis 2018; 39:2642-2654. [PMID: 30101986 PMCID: PMC6282972 DOI: 10.1002/elps.201800082] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/07/2018] [Accepted: 07/23/2018] [Indexed: 11/09/2022]
Abstract
DNA sequencing, starting with Sanger's chain termination method in 1977 and evolving into the next generation sequencing (NGS) techniques of today that employ massively parallel sequencing (MPS), has become essential in application areas such as biotechnology, virology, and medical diagnostics. Reflected by the growing number of articles published over the last 2-3 years, these techniques have also gained attention in the forensic field. This review contains a brief description of first, second, and third generation sequencing techniques, and focuses on the recent developments in human DNA analysis applicable in the forensic field. Relevance to the forensic analysis is that besides generation of standard STR-profiles, DNA repeats can also be sequenced to look for polymorphisms. Furthermore, additional SNPs can be sequenced to acquire information on ancestry, paternity or phenotype. The current MPS systems are also very helpful in cases where only a limited amount of DNA or highly degraded DNA has been secured from a crime scene. If enough autosomal DNA is not present, mitochondrial DNA can be sequenced for maternal lineage analysis. These developments clearly demonstrate that the use of NGS will grow into an indispensable tool for forensic science.
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Affiliation(s)
- Brigitte Bruijns
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
- Life ScienceEngineering & DesignSaxion University of Applied SciencesEnschedeThe Netherlands
| | - Roald Tiggelaar
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
- NanoLab cleanroom, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
| | - Han Gardeniers
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
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Fang C, Zhao J, Liu X, Zhang J, Cao Y, Yang Y, Yu C, Zhang X, Qian J, Liu W, Wu H, Yan J. MicroRNA profile analysis for discrimination of monozygotic twins using massively parallel sequencing and real-time PCR. Forensic Sci Int Genet 2018; 38:23-31. [PMID: 30321748 DOI: 10.1016/j.fsigen.2018.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/22/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022]
Abstract
In general, it is extremely problematic to discriminate between monozygotic twins (MZTs), who share the same genomic DNA sequence, using traditional DNA-based identification methods such as short tandem repeat profiling. MicroRNAs (miRNAs) have shown potential in forensic applications owing to their low molecular weight, abundant and tissue-specific expression. In this study, we utilized massively parallel sequencing technology to perform genome-wide profiling of miRNAs in the blood from four pairs of healthy MZTs. On average, 158 miRNAs were detected in each individual and 14% of which were differentially expressed within each pair of MZTs. The miRNAs with the most significant differences in expression between the twins were confirmed using real-time polymerase chain reaction. Our results demonstrated that miRNAs have potential for use as molecular markers in MZTs discrimination.
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Affiliation(s)
- Chen Fang
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Jing Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100010, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xu Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Jingjing Zhang
- Beijing Huayan Judicial Authentication Institute, Beijing 100192, PR China
| | - Yunwang Cao
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China
| | - Yaran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100010, PR China
| | - Chunrui Yu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Xiaoli Zhang
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Jialin Qian
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Wenli Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China; Beijing Gene Medical Laboratory Co., Ltd., Beijing 100094, PR China.
| | - Jiangwei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100010, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China.
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18
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Recent progress, methods and perspectives in forensic epigenetics. Forensic Sci Int Genet 2018; 37:180-195. [PMID: 30176440 DOI: 10.1016/j.fsigen.2018.08.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 01/19/2023]
Abstract
Forensic epigenetics, i.e., investigating epigenetics variation to resolve forensically relevant questions unanswerable with standard forensic DNA profiling has been gaining substantial ground over the last few years. Differential DNA methylation among tissues and individuals has been proposed as useful resource for three forensic applications i) determining the tissue type of a human biological trace, ii) estimating the age of an unknown trace donor, and iii) differentiating between monozygotic twins. Thus far, forensic epigenetic investigations have used a wide range of methods for CpG marker discovery, prediction modelling and targeted DNA methylation analysis, all coming with advantages and disadvantages when it comes to forensic trace analysis. In this review, we summarize the most recent literature on these three main topics of current forensic epigenetic investigations and discuss limitations and practical considerations in experimental design and data interpretation, such as technical and biological biases. Moreover, we provide future perspectives with regard to new research questions, new epigenetic markers and recent technological advances that - as we envision - will move the field towards forensic epigenomics in the near future.
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Amorim A, Pinto N. Big data in forensic genetics. Forensic Sci Int Genet 2018; 37:102-105. [PMID: 30142461 DOI: 10.1016/j.fsigen.2018.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/23/2018] [Accepted: 08/01/2018] [Indexed: 12/16/2022]
Abstract
The potential and difficulties of the application of genome wide data in forensics are analyzed. We argue that, besides statistical, computational, ethical, economic and technical validation problems, the state of the art of population genetics theory is insufficient to deal with the forensic use of this type of data. In order to keep the current standards of quantifying and reporting genetic evidence, namely in kinship analyses and identification, substantial improvement in the theoretical framework should be reached, since to obtain genome-wide results is to provide the experts with data that they cannot quantify the corresponding evidentiary value. Therefore, while a satisfactory, generalized theoretical and biostatistical modelling is not achieved, it may well be wiser to improve the already established approaches to a limited, pre-defined number of validated genetic markers, amenable to a consensual handling and reporting. Whole genome population analyses will prove extremely useful in selecting the best suited and most efficient of those markers.
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Affiliation(s)
- António Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, Porto, Portugal; Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, Porto, Portugal; CMUP, Centro de Matemática da Universidade do Porto, Porto, Portugal.
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20
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Chaitanya L, Breslin K, Zuñiga S, Wirken L, Pośpiech E, Kukla-Bartoszek M, Sijen T, Knijff PD, Liu F, Branicki W, Kayser M, Walsh S. The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation. Forensic Sci Int Genet 2018; 35:123-135. [DOI: 10.1016/j.fsigen.2018.04.004] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/05/2018] [Accepted: 04/06/2018] [Indexed: 11/29/2022]
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Hussing C, Bytyci R, Huber C, Morling N, Børsting C. The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit. Int J Legal Med 2018; 133:325-334. [PMID: 29797283 DOI: 10.1007/s00414-018-1854-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/11/2018] [Indexed: 10/24/2022]
Abstract
Some STR loci have internal sequence variations, which are not revealed by the standard STR typing methods used in forensic genetics (PCR and fragment length analysis by capillary electrophoresis (CE)). Typing of STRs with next-generation sequencing (NGS) uncovers the sequence variation in the repeat region and in the flanking regions. In this study, 363 Danish individuals were typed for 56 STRs (26 autosomal STRs, 24 Y-STRs, and 6 X-STRs) using the ForenSeq™ DNA Signature Prep Kit to establish a Danish STR sequence database. Increased allelic diversity was observed in 34 STRs by the PCR-NGS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were around four times larger than the numbers of alleles determined by repeat length alone. Thirteen SNPs and one InDel were identified in the flanking regions of 12 STRs. Furthermore, 36 single positions and five longer stretches in the STR flanking regions were found to have dubious genotyping quality. The combined match probability of the 26 autosomal STRs was 10,000 times larger using the PCR-NGS assay than by using PCR-CE. The typical paternity indices for trios and duos were 500 and 100 times larger, respectively, than those obtained with PCR-CE. The assay also amplified 94 SNPs selected for human identification. Eleven of these loci were not in Hardy-Weinberg equilibrium in the Danish population, most likely because the minimum threshold for allele calling (30 reads) in the ForenSeq™ Universal Analysis Software was too low and frequent allele dropouts were not detected.
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Affiliation(s)
- C Hussing
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark
| | - R Bytyci
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark
| | - C Huber
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark.
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