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Syndercombe Court D. Alec Samuels (1930-2022). Med Sci Law 2023; 63:341. [PMID: 37350062 DOI: 10.1177/00258024231182590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
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2
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Davenport L, Devesse L, Syndercombe Court D, Ballard D. Forensic identity SNPs: Characterisation of flanking region variation using massively parallel sequencing. Forensic Sci Int Genet 2023; 64:102847. [PMID: 36863275 DOI: 10.1016/j.fsigen.2023.102847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
Single nucleotide polymorphisms (SNPs) can be analysed for identity or kinship applications in forensic genetics to either provide an adjunct to traditional STR typing or as a stand-alone approach. The advent of massively parallel sequencing technology (MPS) has provided a useful opportunity to more easily deploy SNP typing in a forensic context, given the ability to simultaneously amplify a large number of markers. Furthermore, MPS also provides valuable sequence data for the targeted regions, which enables the detection of any additional variation seen in the flanking regions of amplicons. In this study we genotyped 977 samples across five UK-relevant population groups (White British, East Asian, South Asian, North-East African and West African) for 94 identity-informative SNP markers using the ForenSeq DNA Signature Prep Kit. Examination of flanking region variation allowed for the identification of 158 additional alleles across all populations studied. Here we present allele frequencies for all 94 identity-informative SNPs, both including and excluding the flanking region sequence of these markers. We also present information on the configuration of these SNPs in the ForenSeq DNA Signature Prep Kit, including performance metrics for the markers and investigation of bioinformatic and chemistry-based discordances. Overall, the inclusion of flanking region variation in the analysing workflow for these markers reduced the average combined match probability 2175 times across all populations, with a maximum reduction of 675,000-fold in the West African population. The gain due to flanking region-based discrimination increased the heterozygosity of some loci above that of some of the least useful forensic STR loci; thus demonstrating the benefit of enhanced analysis of currently targeted SNP markers for forensic applications.
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Affiliation(s)
- Lucinda Davenport
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
| | - Laurence Devesse
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Denise Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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3
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Mallinder B, Pope S, Thomson J, Beck LA, McDonald A, Ramsbottom D, Court DS, Vanhinsbergh D, Barber M, Evett I, Sullivan K, Whitaker J. Interpretation and reporting of mixed DNA profiles by seven forensic laboratories in the UK and Ireland. Forensic Sci Int Genet 2022; 58:102674. [DOI: 10.1016/j.fsigen.2022.102674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
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4
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Aliferi A, Sundaram S, Ballard D, Freire-Aradas A, Phillips C, Lareu MV, Court DS. Combining current knowledge on DNA methylation-based age estimation towards the development of a superior forensic DNA intelligence tool. Forensic Sci Int Genet 2021; 57:102637. [PMID: 34852982 DOI: 10.1016/j.fsigen.2021.102637] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 01/09/2023]
Abstract
The estimation of chronological age from biological fluids has been an important quest for forensic scientists worldwide, with recent approaches exploiting the variability of DNA methylation patterns with age in order to develop the next generation of forensic 'DNA intelligence' tools for this application. Drawing from the conclusions of previous work utilising massively parallel sequencing (MPS) for this analysis, this work introduces a DNA methylation-based age estimation method for blood that exhibits the best combination of prediction accuracy and sensitivity reported to date. Statistical evaluation of markers from 51 studies using microarray data from over 4000 individuals, followed by validation using in-house generated MPS data, revealed a final set of 11 markers with the greatest potential for accurate age estimation from minimal DNA material. Utilising an algorithm based on support vector machines, the proposed model achieved an average error (MAE) of 3.3 years, with this level of accuracy retained down to 5 ng of starting DNA input (~ 1 ng PCR input). The accuracy of the model was retained (MAE = 3.8 years) in a separate test set of 88 samples of Spanish origin, while predictions for donors of greater forensic interest (< 55 years of age) displayed even higher accuracy (MAE = 2.6 years). Finally, no sex-related bias was observed for this model, while there were also no signs of variation observed between control and disease-associated populations for schizophrenia, rheumatoid arthritis, frontal temporal dementia and progressive supranuclear palsy in microarray data relating to the 11 markers.
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Affiliation(s)
- Anastasia Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Sudha Sundaram
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Denise Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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5
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Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021; 184:3376-3393.e17. [PMID: 34043940 PMCID: PMC8238498 DOI: 10.1016/j.cell.2021.05.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023]
Abstract
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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Affiliation(s)
- David Danko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Evan E Afshin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Chandrima Bhattacharya
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniel J Butler
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Kern Rei Chng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Daisy Donnellan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Katelyn Jackson
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Katerina Kuchin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Mikhail Karasikov
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail Lyons
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Lauren Mak
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dmitry Meleshko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Harun Mustafa
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Beth Mutai
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya
| | - Russell Y Neches
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Ng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | | | | | - Eileen Png
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Krista A Ryon
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jorge L Sanchez
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Heba Shaaban
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Maria A Sierra
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dominique Thomas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Ben Young
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Omar O Abudayyeh
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Josue Alicea
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | | | - Eduardo Castro-Nallar
- Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Ana M Cañas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Aspassia D Chatziefthimiou
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Youping Deng
- University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Christelle Desnues
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Emmanuel Dias-Neto
- Medical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil
| | - Marius Dybwad
- Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Dennis Gankin
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | | | - David C Green
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Iman Hajirasouliha
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jaden J A Hastings
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago, Chile; Wellcome Sanger Institute, Hinxton, UK
| | | | - Andre Kahles
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; Kyiv Academic University, Kyiv, Ukraine; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Frank J Kelly
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Kaymisha Knights
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paweł P Łabaj
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Boku University Viennna, Vienna, Austria
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Ken McGrath
- Microba, 388 Queen St, Brisbane City, QLD 4000, Australia
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | | | - Houtan Noushmehr
- University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto - SP, Brazil
| | - Manuela Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
| | - Orhan Özcan
- Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicolás Rascovan
- Microbial Paleogenomics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - Hugues Richard
- Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France; Robert Koch Institute, Berlin, Germany
| | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Rania Siam
- University of Medicine and Health Sciences, St. Kitts, West Indies and American University in Cairo, Cairo, Egypt
| | - Le Huu Song
- 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | | | - Denise Syndercombe Court
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | | | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Klas I Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; SciLife EVP, Department of Aquatic Sciences Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Brandon Valentine
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dimitar I Vassilev
- Faculty of Mathematics and Informatics, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Elena M Vayndorf
- Institute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, AK, USA
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Univeristätsklinikum Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam
| | - Jun Wu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Jifeng Zhu
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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6
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Syndercombe Court D. Protecting against racial bias in DNA databasing. Nat Comput Sci 2021; 1:249-250. [PMID: 38217175 DOI: 10.1038/s43588-021-00064-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
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7
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Devesse L, Davenport L, Borsuk L, Gettings K, Mason-Buck G, Vallone PM, Syndercombe Court D, Ballard D. Classification of STR allelic variation using massively parallel sequencing and assessment of flanking region power. Forensic Sci Int Genet 2020; 48:102356. [PMID: 32712568 DOI: 10.1016/j.fsigen.2020.102356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
The application of massively parallel sequencing (MPS) to forensic genetics has led to improvements in multiple aspects of DNA analysis, however, additional complexities are concurrently associated with these advances. In relation to short tandem repeat (STR) typing, the move to sequence rather than length-based methodologies has highlighted the extent to which previous allelic variation was masked - both within and outside of the repeat regions (the flanking regions). In order to fully implement MPS for autosomal STR analysis, sequence-based allelic frequencies must be available, and concordance with previous typing techniques needs to be assessed. In this work, a series of samples (n = 1007) from five different population groups were genotyped using the MiSeq FGx™ Forensic Genomics System. Results were compared to those obtained using capillary electrophoresis (CE), and sequence variation has been characterised both within and outside STR repeat regions, with allelic frequencies provided for all variants observed within this database. Analysing and characterising flanking region sequence is currently less straightforward than studying repeat region variation alone, and the added value of doing so remains largely unexplored - this paper provides data to show that the gain in polymorphism achieved when analysing flanking regions is less than might be expected. In the White British population for example, including the sequence variation within repeat regions of 26 autosomal STRs made the average combined random match probability (RMP) over 700 times lower than with length-based alleles alone. Including the sequence variation within the flanking regions only resulted in a combined RMP that was a further 4 times lower.
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Affiliation(s)
- Laurence Devesse
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK.
| | - Lucinda Davenport
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK
| | - Lisa Borsuk
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Katherine Gettings
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Gabriella Mason-Buck
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK
| | - Peter M Vallone
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Denise Syndercombe Court
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK
| | - David Ballard
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK
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8
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Phillips C, Devesse L, Ballard D, van Weert L, de la Puente M, Melis S, Álvarez Iglesias V, Freire-Aradas A, Oldroyd N, Holt C, Syndercombe Court D, Carracedo Á, Lareu MV. Global patterns of STR sequence variation: Sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit. Electrophoresis 2018; 39:2708-2724. [DOI: 10.1002/elps.201800117] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 07/02/2018] [Accepted: 07/26/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Christopher Phillips
- Forensic Genetics Unit; Institute of Forensic Sciences; University of Santiago de Compostela; Galicia Spain
| | - Laurence Devesse
- King's Forensics; King's College London; London UK
- Verogen Inc.; San Diego USA
| | | | - Leanne van Weert
- Forensic Genetics Unit; Institute of Forensic Sciences; University of Santiago de Compostela; Galicia Spain
| | - Maria de la Puente
- Forensic Genetics Unit; Institute of Forensic Sciences; University of Santiago de Compostela; Galicia Spain
| | - Stefania Melis
- Forensic Genetics Unit; Institute of Forensic Sciences; University of Santiago de Compostela; Galicia Spain
| | - Vanessa Álvarez Iglesias
- Forensic Genetics Unit; Institute of Forensic Sciences; University of Santiago de Compostela; Galicia Spain
| | - Ana Freire-Aradas
- Forensic Genetics Unit; Institute of Forensic Sciences; University of Santiago de Compostela; Galicia Spain
| | | | | | | | - Ángel Carracedo
- Forensic Genetics Unit; Institute of Forensic Sciences; University of Santiago de Compostela; Galicia Spain
- Genomic Medicine Group; University of Santiago de Compostela; Galicia Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit; Institute of Forensic Sciences; University of Santiago de Compostela; Galicia Spain
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9
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Aliferi A, Thomson J, McDonald A, Paynter VM, Ferguson S, Vanhinsbergh D, Syndercombe Court D, Ballard D. UK and Irish Y-STR population data—A catalogue of variant alleles. Forensic Sci Int Genet 2018; 34:e1-e6. [DOI: 10.1016/j.fsigen.2018.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 12/09/2022]
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10
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Vidaki A, Ballard D, Aliferi A, Miller TH, Barron LP, Syndercombe Court D. DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing. Forensic Sci Int Genet 2017; 28:225-236. [PMID: 28254385 PMCID: PMC5392537 DOI: 10.1016/j.fsigen.2017.02.009] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/07/2017] [Accepted: 02/16/2017] [Indexed: 12/19/2022]
Abstract
Blood DNA methylation profiles of 1156 individuals were assessed for age correlation. Stepwise regression identified 23 age-associated CpG sites in DNA from blood. A machine learning model based on 16 markers predicted age with a mean error of 3.8 years. The model predicted age successfully for twins and ‘diseased’ individuals. A new NGS-based method was combined with machine learning for age prediction.
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person’s lifetime including epigenetic patterns. The aim of this study was to use age-specific DNA methylation patterns to generate an accurate model for the prediction of chronological age using data from whole blood. In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156 whole blood samples (aged 2–90 years) analysed with Illumina’s genome-wide methylation platforms (27 K/450 K). Applying stepwise regression for variable selection, 23 of these CpG sites were identified that could significantly contribute to age prediction modelling and multiple regression analysis carried out with these markers provided an accurate prediction of age (R2 = 0.92, mean absolute error (MAE) = 4.6 years). However, applying machine learning, and more specifically a generalised regression neural network model, the age prediction significantly improved (R2 = 0.96) with a MAE = 3.3 years for the training set and 4.4 years for a blind test set of 231 cases. The machine learning approach used 16 CpG sites, located in 16 different genomic regions, with the top 3 predictors of age belonged to the genes NHLRC1, SCGN and CSNK1D. The proposed model was further tested using independent cohorts of 53 monozygotic twins (MAE = 7.1 years) and a cohort of 1011 disease state individuals (MAE = 7.2 years). Furthermore, we highlighted the age markers’ potential applicability in samples other than blood by predicting age with similar accuracy in 265 saliva samples (R2 = 0.96) with a MAE = 3.2 years (training set) and 4.0 years (blind test). In an attempt to create a sensitive and accurate age prediction test, a next generation sequencing (NGS)-based method able to quantify the methylation status of the selected 16 CpG sites was developed using the Illumina MiSeq® platform. The method was validated using DNA standards of known methylation levels and the age prediction accuracy has been initially assessed in a set of 46 whole blood samples. Although the resulted prediction accuracy using the NGS data was lower compared to the original model (MAE = 7.5 years), it is expected that future optimization of our strategy to account for technical variation as well as increasing the sample size will improve both the prediction accuracy and reproducibility.
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Affiliation(s)
- Athina Vidaki
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK.
| | - David Ballard
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK.
| | - Anastasia Aliferi
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK
| | - Thomas H Miller
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK
| | - Leon P Barron
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK
| | - Denise Syndercombe Court
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK
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11
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Vidaki A, Giangasparo F, Syndercombe Court D. Discovery of potential DNA methylation markers for forensic tissue identification using bisulphite pyrosequencing. Electrophoresis 2016; 37:2767-2779. [DOI: 10.1002/elps.201600261] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Athina Vidaki
- Department of Pharmacy and Forensic Science; King's College London; Franklin-Wilkins Building London UK
| | - Federica Giangasparo
- Department of Pharmacy and Forensic Science; King's College London; Franklin-Wilkins Building London UK
| | - Denise Syndercombe Court
- Department of Pharmacy and Forensic Science; King's College London; Franklin-Wilkins Building London UK
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12
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Murray A, Letourneau A, Canzonetta C, Stathaki E, Gimelli S, Sloan-Bena F, Abrehart R, Goh P, Lim S, Baldo C, Dagna-Bricarelli F, Hannan S, Mortensen M, Ballard D, Syndercombe Court D, Fusaki N, Hasegawa M, Smart TG, Bishop C, Antonarakis SE, Groet J, Nizetic D. Brief report: isogenic induced pluripotent stem cell lines from an adult with mosaic down syndrome model accelerated neuronal ageing and neurodegeneration. Stem Cells 2016; 33:2077-84. [PMID: 25694335 PMCID: PMC4737213 DOI: 10.1002/stem.1968] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/17/2015] [Indexed: 01/11/2023]
Abstract
Trisomy 21 (T21), Down Syndrome (DS) is the most common genetic cause of dementia and intellectual disability. Modeling DS is beginning to yield pharmaceutical therapeutic interventions for amelioration of intellectual disability, which are currently being tested in clinical trials. DS is also a unique genetic system for investigation of pathological and protective mechanisms for accelerated ageing, neurodegeneration, dementia, cancer, and other important common diseases. New drugs could be identified and disease mechanisms better understood by establishment of well-controlled cell model systems. We have developed a first nonintegration-reprogrammed isogenic human induced pluripotent stem cell (iPSC) model of DS by reprogramming the skin fibroblasts from an adult individual with constitutional mosaicism for DS and separately cloning multiple isogenic T21 and euploid (D21) iPSC lines. Our model shows a very low number of reprogramming rearrangements as assessed by a high-resolution whole genome CGH-array hybridization, and it reproduces several cellular pathologies seen in primary human DS cells, as assessed by automated high-content microscopic analysis. Early differentiation shows an imbalance of the lineage-specific stem/progenitor cell compartments: T21 causes slower proliferation of neural and faster expansion of hematopoietic lineage. T21 iPSC-derived neurons show increased production of amyloid peptide-containing material, a decrease in mitochondrial membrane potential, and an increased number and abnormal appearance of mitochondria. Finally, T21-derived neurons show significantly higher number of DNA double-strand breaks than isogenic D21 controls. Our fully isogenic system therefore opens possibilities for modeling mechanisms of developmental, accelerated ageing, and neurodegenerative pathologies caused by T21.
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Affiliation(s)
- Aoife Murray
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom.,The LonDownS Consortium, Wellcome Trust, London, United Kingdom
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Claudia Canzonetta
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom
| | - Elisavet Stathaki
- Service of Genetic Medicine, University Geneva Hospitals, Geneva, Switzerland
| | - Stefania Gimelli
- Service of Genetic Medicine, University Geneva Hospitals, Geneva, Switzerland
| | | | - Robert Abrehart
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom
| | - Pollyanna Goh
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom.,The LonDownS Consortium, Wellcome Trust, London, United Kingdom
| | - Shuhui Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Chiara Baldo
- Human Genetics Laboratory, Galliera Hospital, Genoa, Italy
| | | | - Saad Hannan
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Martin Mortensen
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - David Ballard
- Department of Forensic and Analytical Science, King's College, London, United Kingdom
| | | | - Noemi Fusaki
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | | | - Trevor G Smart
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Cleo Bishop
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jürgen Groet
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom.,Stem Cell Laboratory, National Centre for Bowel Research and Surgical Innovation, Queen Mary University of London, London, United Kingdom.,The LonDownS Consortium, Wellcome Trust, London, United Kingdom
| | - Dean Nizetic
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom.,The LonDownS Consortium, Wellcome Trust, London, United Kingdom.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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13
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Abstract
We estimate the population genetics parameter (also referred to as the fixation index) from short tandem repeat (STR) allele frequencies, comparing many worldwide human subpopulations at approximately the national level with continental-scale populations. is commonly used to measure population differentiation, and is important in forensic DNA analysis to account for remote shared ancestry between a suspect and an alternative source of the DNA. We estimate comparing subpopulations with a hypothetical ancestral population, which is the approach most widely used in population genetics, and also compare a subpopulation with a sampled reference population, which is more appropriate for forensic applications. Both estimation methods are likelihood-based, in which is related to the variance of the multinomial-Dirichlet distribution for allele counts. Overall, we find low values, with posterior 97.5 percentiles when comparing a subpopulation with the most appropriate population, and even for inter-population comparisons we find . These are much smaller than single nucleotide polymorphism-based inter-continental estimates, and are also about half the magnitude of STR-based estimates from population genetics surveys that focus on distinct ethnic groups rather than a general population. Our findings support the use of up to 3% in forensic calculations, which corresponds to some current practice.
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14
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Dawnay N, Hughes R, Court DS, Duxbury N. Species detection using HyBeacon(®) probe technology: Working towards rapid onsite testing in non-human forensic and food authentication applications. Forensic Sci Int Genet 2015; 20:103-111. [PMID: 26561743 DOI: 10.1016/j.fsigen.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 10/05/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Identifying individual species or determining species' composition in an unknown sample is important for a variety of forensic applications. Food authentication, monitoring illegal trade in endangered species, forensic entomology, sexual assault case work and counter terrorism are just some of the fields that can require the detection of the biological species present. Traditional laboratory based approaches employ a wide variety of tools and technologies and exploit a number of different species specific traits including morphology, molecular differences and immuno-chemical analyses. A large number of these approaches require laboratory based apparatus and results can take a number of days to be returned to investigating authorities. Having a presumptive test for rapid identification could lead to savings in terms of cost and time and allow sample prioritisation if confirmatory testing in a laboratory is required later. This model study describes the development of an assay using a single HyBeacon(®) probe and melt curve analyses allowing rapid screening and authentication of food products labelled as Atlantic cod (Gadus morhua). Exploiting melt curve detection of species specific SNP sites on the COI gene the test allows detection of a target species (Atlantic cod) and closely related species which may be used as substitutes. The assay has been designed for use with the Field Portable ParaDNA system, a molecular detection platform for non-expert users. The entire process from sampling to result takes approximately 75min. Validation studies were performed on both single source genomic DNA, mixed genomic DNA and commercial samples. Data suggests the assay has a lower limit of detection of 31 pg DNA. The specificity of the assay to Atlantic cod was measured by testing highly processed food samples including frozen, defrosted and cooked fish fillets as well as fish fingers, battered fish fillet and fish pie. Ninety-six (92.7%) of all Atlantic cod food products, tested, provided a correct single species result with the remaining samples erroneously identified as containing non-target species. The data shows that the assay was quick to design and characterise and is also capable of yielding results that would be beneficial in a variety of fields, not least the authentication of food.
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Affiliation(s)
- Nick Dawnay
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon OX14 3ED, UK; School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK.
| | - Rebecca Hughes
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Denise Syndercombe Court
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Nicola Duxbury
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon OX14 3ED, UK
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15
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Brayley-Morris H, Sorrell A, Revoir AP, Meakin GE, Court DS, Morgan RM. Persistence of DNA from laundered semen stains: Implications for child sex trafficking cases. Forensic Sci Int Genet 2015; 19:165-171. [PMID: 26232275 DOI: 10.1016/j.fsigen.2015.07.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 06/22/2015] [Accepted: 07/14/2015] [Indexed: 10/23/2022]
Abstract
In sexual assault cases, particularly those involving internal child sex trafficking (ICST), victims often hide their semen-stained clothing. This can result in a lag time of several months before the items are laundered and subsequently seized during a criminal investigation. Although it has been demonstrated previously that DNA can be recovered from clothing washed immediately after semen deposition, laundered items of clothing are not routinely examined in ICST cases, due to the assumption that the time delay and washing would result in no detectable DNA. The aim of this study was to examine whether viable DNA profiles could be recovered from laundered semen stains where there has been a significant lag time between semen deposition from one or more individuals and one or more washes of the stained clothing. Items of UK school uniform (T-shirts, trousers, tights) were stained with fresh semen (either from a single donor or a 1:1 mixture from two donors) and stored in a wardrobe for eight months. Stained and unstained items (socks) were then washed at 30 °C or 60 °C and with non-biological or biological detergent. DNA samples extracted from the semen-stained sites and from the unstained socks were quantified and profiled. High quantities of DNA, (6-18 μg) matching the DNA profiles of the semen donors, were recovered from all semen-stained clothing that had been laundered once, irrespective of wash conditions. This quantity,and profile quality,did not decline significantly with multiple washes. The two donor semen samples yielded ∼ 10-fold more DNA from the T-shirts than from the trousers. This disparity resulted in the T-shirts yielding a ∼ 1:1 mixture of DNA from the two donors, whereas the trousers yielded a major DNA profile matching only that of the second donor. The quantities of DNA recovered from the unstained socks were an order of magnitude lower, with most of the DNA being attributable to the donor of the semen on the stained clothing within the same wash, demonstrating the transfer of semen-derived DNA among items of clothing in the washing machine. This study demonstrates that complete DNA profiles can be obtained from laundered semen stains on school uniform-type clothing, with an eight-month lag time between semen deposition and laundering, despite multiple washes and stains from two semen donors. These data emphasise the need to recover and examine the clothing of victims for semen and DNA evidence, even if the clothing has been stored for several months or washed multiple times since the sexual offence took place.
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Affiliation(s)
- Helen Brayley-Morris
- UCL Centre for the Forensic Sciences, 35 Tavistock Square, London WC1H 9EZ, UK; UCL Department of Security and Crime Science, 35 Tavistock Square, London WC1H 9EZ, UK
| | - Amber Sorrell
- UCL Department of Security and Crime Science, 35 Tavistock Square, London WC1H 9EZ, UK
| | - Andrew P Revoir
- Faculty of Life Sciences and Medicine, KCL, Franklin-Wilkins Building, London SE1 9NH, UK
| | - Georgina E Meakin
- UCL Centre for the Forensic Sciences, 35 Tavistock Square, London WC1H 9EZ, UK; UCL Department of Security and Crime Science, 35 Tavistock Square, London WC1H 9EZ, UK
| | | | - Ruth M Morgan
- UCL Centre for the Forensic Sciences, 35 Tavistock Square, London WC1H 9EZ, UK; UCL Department of Security and Crime Science, 35 Tavistock Square, London WC1H 9EZ, UK.
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16
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Devesse L, Syndercombe Court D, Cowan D. Determining the authenticity of athlete urine in doping control by DNA analysis. Drug Test Anal 2015; 7:912-8. [DOI: 10.1002/dta.1785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 01/23/2015] [Accepted: 02/12/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Laurence Devesse
- The Drug Control Centre; King's College London, Franklin-Wilkins Building; 150 Stamford Street London SE1 9NH UK
| | - Denise Syndercombe Court
- The Drug Control Centre; King's College London, Franklin-Wilkins Building; 150 Stamford Street London SE1 9NH UK
| | - David Cowan
- The Drug Control Centre; King's College London, Franklin-Wilkins Building; 150 Stamford Street London SE1 9NH UK
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17
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Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SMT, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MHD, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RSM, Nogueira TLS, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MMD, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MCD, Rodriguez JJR, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LSD, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RYY, Krawczak M, Nothnagel M, Roewer L. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int Genet 2014; 12:12-23. [PMID: 24854874 PMCID: PMC4127773 DOI: 10.1016/j.fsigen.2014.04.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/19/2014] [Indexed: 02/05/2023]
Abstract
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
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Affiliation(s)
- Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Sabine Siegert
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Cíntia Alves
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Renato Salazar
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | | | - Lorna H Santos
- Philippine National Police Crime Laboratory, Quezon City, Philippines
| | - Katja Anslinger
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Birgit Bayer
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Wei Wei
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | | | - Balazs Egyed
- GenoID Forensic DNA Laboratory, Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Beate Balitzki
- Institut für Rechtsmedizin, Universität Basel, Switzerland
| | | | - David Ballard
- Department of Forensic and Analytical Science, King's College London, London, UK
| | | | - Xinia Barrantes
- Forensic Sciences Department, Poder Judicial, Heredia, Costa Rica
| | | | - Tina Wiest
- Landeskriminalamt Baden-Württemberg, Germany
| | - Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | | | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA
| | - Carey Davis
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA
| | - Bruce Budowle
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Helen Burri
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | - Urs Borer
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | | | - Elizeu F Carvalho
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | - Patricia M Domingues
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | | | - Michael D Coble
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Carolyn R Hill
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Daniel Corach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Mariela Caputo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Maria E D'Amato
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Sean Davison
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Ronny Decorte
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Maarten H D Larmuseau
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Claudio Ottoni
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Olga Rickards
- Centre of Molecular Antropology For Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Italy
| | - Di Lu
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Chengtao Jiang
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Tadeusz Dobosz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - Anna Jonkisz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - William E Frank
- Illinois State Police, Research & Development Laboratory, Springfield, USA
| | - Ivana Furac
- Department of Forensic Medicine and Criminology, University of Zagreb, Croatia
| | - Christian Gehrig
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Vincent Castella
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Branka Grskovic
- Forensic Science Centre "Ivan Vucetic", General Police Directorate, Ministry of Interior, Zagreb, Croatia
| | - Cordula Haas
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | - Jana Wobst
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | | | | | - Katsuya Honda
- Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, Japan
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Di Zhou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Yan Li
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | - Shenglan Chen
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | | | | | - Zlatko Jakovski
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Tanja Ilievska
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Anja E Klann
- Institut für Rechtsmedizin, Universitätsmedizin Greifswald, Germany
| | | | - Peter de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thirsa Kraaijenbrink
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aikaterini Kondili
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Penelope Miniati
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Maria Vouropoulou
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Lejla Kovacevic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanovic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Iris Lindner
- Institut für Rechtsmedizin, Universität Rostock, Germany
| | - Issam Mansour
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Mouayyad Al-Azem
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Ansar El Andari
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Miguel Marino
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Sandra Furfuro
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Laura Locarno
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Pablo Martín
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Gracia M Luque
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Antonio Alonso
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | | | - Helena Moreira
- Departamento de Biologia, Universidade de Aveiro, Portugal
| | - Natsuko Mizuno
- National Research Institute of Police Science, Chiba, Japan
| | | | - Rodrigo S Moura Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro and DIMAV/INMETRO, Brazil
| | | | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | | | | | - Michael Kohl
- Institut für Rechtsmedizin, Universität Leipzig, Germany
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xianping Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | - Baowen Cheng
- Department of Criminal Investigation, Yunnan Provincial Public Security Bureau, Kunming, China
| | - Carolina Núñez
- BIOMICs Research Group, Universidad del País Vasco, Vitoria, Spain
| | | | - Jill K Olofsson
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Valerio Onofri
- Section of Legal Medicine, Università Politecnica delle Marche, Ancona, Italy
| | | | - Horolma Pamjav
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Antonia Volgyi
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Gusztav Barany
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Ryszard Pawlowski
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Agnieszka Maciejewska
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Susi Pelotti
- Department of Medical and Surgical Sciences (DIMEC), Institute of Legal Medicine, School of Medicine, University of Bologna, Italy
| | - Witold Pepinski
- Department of Forensic Medicine, Medical University of Bialystok, Poland
| | | | - Christopher Phillips
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Jorge Cárdenas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Danel Rey-Gonzalez
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Francesca Brisighelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Department of Zoology, University of Oxford, Oxford, UK
| | - Ulises Toscanini
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | - Andrea Piccinini
- Forensic Genetics Laboratory, Department of Human Morphology and Biomedical Sciences, Università degli Studi di Milano, Italy
| | - Marilidia Piglionica
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Stefania L Baldassarra
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Poland
| | | | | | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - Antti Sajantila
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Department of Forensic Medicine, University of Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Evelyn Guevara
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Jazelyn Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Maria Corazon De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Jae Joseph Russell Rodriguez
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Institute of Biological Sciences, University of the Philippines Los Baños, Laguna, Philippines
| | - Ulrike Schmidt
- Institut für Rechtsmedizin, Universitätsklinikum Freiburg, Germany
| | | | - Pekka Saukko
- Department of Forensic Medicine, University of Turku, Finland
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Miriam Sirker
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Yu Na Oh
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Iulia Skitsa
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Alexandra Ampati
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Tobi-Gail Smith
- Department of Basic Medical Sciences, University of the West Indies, Kingston, Jamaica
| | | | - Vlastimil Stenzl
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Thomas Capal
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Helena Nilsson
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Stefania Turrina
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Domenico De Leo
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Andrea Verzeletti
- Istituto di Medicina Legale, Universitá degli Studi di Brescia, Italy
| | | | - Jon H Wetton
- Department of Genetics, University of Leicester, UK
| | | | | | | | | | | | - Rita Y Y Yong
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.
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Phillips C, Gelabert-Besada M, Fernandez-Formoso L, García-Magariños M, Santos C, Fondevila M, Ballard D, Syndercombe Court D, Carracedo Á, Victoria Lareu M. “New turns from old STaRs”: Enhancing the capabilities of forensic short tandem repeat analysis. Electrophoresis 2014; 35:3173-87. [DOI: 10.1002/elps.201400095] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/25/2014] [Accepted: 05/15/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Miguel Gelabert-Besada
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Luis Fernandez-Formoso
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | | | - Carla Santos
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Manuel Fondevila
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - David Ballard
- Department of Forensic and Analytical Science; King's College London; London UK
| | | | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
- Center of Excellence in Genomic Medicine Research; King Abdulaziz University; Jeddah Saudi Arabia
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
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Vidaki A, Daniel B, Court DS. Forensic DNA methylation profiling—Potential opportunities and challenges. Forensic Sci Int Genet 2013; 7:499-507. [DOI: 10.1016/j.fsigen.2013.05.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/14/2013] [Indexed: 11/26/2022]
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Court DS. Low copy number DNA: where next? Med Sci Law 2010; 50:55-56. [PMID: 20593594 DOI: 10.1258/msl.2010.010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Phillips C, Barbaro A, Formoso LF, Ballard D, Court DS, Carracedo Á, Lareu M. Development and validation of a next generation STR ESS-pentaplex. Forensic Science International: Genetics Supplement Series 2009. [DOI: 10.1016/j.fsigss.2009.08.190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Syndercombe Court D, Kelsell DP. Human genetics. Med Sci (Basel) 2009. [DOI: 10.1016/b978-0-7020-2679-9.00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Syndercombe Court D, Domizio P, Yeatman N. Pathology and immunology. Med Sci (Basel) 2009. [DOI: 10.1016/b978-0-7020-2679-9.00006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Musgrave-Brown E, Ballard D, Álvarez MF, Fang R, Harrison C, Phillips C, Prasad Y, Rey BS, Thacker C, Wiluhn J, Carracedo A, Schneider PM, Court DS. Forensic validation of the Genplex SNP typing system—Results of an inter-laboratory study. Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Musgrave-Brown E, Ballard D, Balogh K, Bender K, Berger B, Bogus M, Børsting C, Brion M, Fondevila M, Harrison C, Oguzturun C, Parson W, Phillips C, Proff C, Ramos-Luis E, Sanchez JJ, Diz PS, Rey BS, Stradmann-Bellinghausen B, Thacker C, Carracedo A, Morling N, Scheithauer R, Schneider PM, Court DS. Forensic validation of the SNPforID 52-plex assay. Forensic Sci Int Genet 2007; 1:186-90. [DOI: 10.1016/j.fsigen.2007.01.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 01/27/2007] [Indexed: 10/23/2022]
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Bjerre A, Court DS, Lincoln P, Morling N. A report of the 1995 and 1996 Paternity Testing Workshops of the English Speaking Working Group of the International Society for Forensic Haemogenetics. Forensic Sci Int 1997; 90:41-55. [PMID: 9438364 DOI: 10.1016/s0379-0738(97)00143-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report the results of the 1995 and 1996 Paternity Testing Workshops of the English Speaking Working Group of the International Society for Forensic Haemogenetics. In 1995, 18 laboratories participated and in 1996, 21 laboratories participated. Each year, blood samples from three persons (child, mother and alleged father) were sent to participating laboratories which performed paternity testing according to their usual protocols. The results and answers to questionnaires concerning methods were compiled and are presented in this report. From the questionnaires, a general tendency to a more frequent use of polymerase chain reaction (PCR) based methods was seen. In 1996, 62% of the laboratories used PCR based methods. Ten per cent of the laboratories used only PCR based methods. The remaining 90% of the laboratories performed restriction fragment length polymorphism (RFLP) investigations of variable numbers of tandem repeat (VNTR) loci with single locus probes (SLPs) either alone or in combination with PCR based typing, multi locus probing, classical systems (ABO etc.), or serological HLA typing. In 1996, typing with classical systems was used in 29% of the laboratories. The majority of the laboratories performed RFLP typing of VNTR loci using very similar methods. The results and the inter-laboratory variations of the measured lengths of the DNA-fragments of the VNTR regions D2S44, D7S21, D7S22, and D12S11 of the trios were analysed. The overall coefficient of variation was 2.15% in 1995 and 1.43% in 1996. During the period 1991-1996, the inter-laboratory variation has decreased, most probably due to the fact that the methods have now been optimised and the majority of the participating laboratories have adopted the standardised method for RFLP typing with SLPs which was agreed upon for investigations in crime cases by the European DNA Profiling Group. In 1996, eight laboratories reported the results of PCR based typing of the short tandem repeat (STR) locus HumTH01, six laboratories reported results of HumVWA31A typing, and five laboratories reported the results of typing of the STR locus HumF13A1 and the VNTR locus D1S80. The results were concordant although the nomenclature was slightly inconsistent concerning the classification of an irregular repeat of the HumTH01 system.
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Affiliation(s)
- A Bjerre
- Department of Forensic Genetics, University of Copenhagen, Denmark
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Drozd MA, Archard L, Lincoln PJ, Morling N, Nellemann LJ, Phillips C, Soteriou B, Court DS. An investigation of the HUMVWA31A locus in British Caucasians. Forensic Sci Int 1994; 69:161-70. [PMID: 7813999 DOI: 10.1016/0379-0738(94)90252-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A number of short tandem repeat (STR) loci are currently being examined for their usefulness as markers of identity; HUMVWA31A is one such locus. We used a high-sieving agarose technique to type 200 British Caucasians for this locus. Comparison of the resultant allele frequencies with other published databases showed that their distributions were similar. Observed heterozygosity was similar to that reported in other population studies but significantly lower than expected. A goodness of fit analysis of observed and expected genotypes was highly significant, suggesting a deviation from Hardy-Weinberg equilibrium, although reports from other populations appeared not to show such differences. The possibility that mistyping had led to an erroneous statistic was investigated by detailed examination of samples within our own laboratory and in two other laboratories, involving verification of the agarose typing by both automated fluorescent detection techniques, and sequencing. Other reported deviations from Hardy-Weinberg equilibrium in STR systems are discussed.
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Affiliation(s)
- M A Drozd
- Department of Haematology, London Hospital Medical College, UK
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