51
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Gill P, Hicks T, Butler JM, Connolly E, Gusmão L, Kokshoorn B, Morling N, van Oorschot RA, Parson W, Prinz M, Schneider PM, Sijen T, Taylor D. DNA commission of the International society for forensic genetics: Assessing the value of forensic biological evidence - Guidelines highlighting the importance of propositions. Part II: Evaluation of biological traces considering activity level propositions. Forensic Sci Int Genet 2020; 44:102186. [DOI: 10.1016/j.fsigen.2019.102186] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 01/27/2023]
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52
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The MASTiFF panel-a versatile multiple-allele SNP test for forensics. Int J Legal Med 2019; 134:441-450. [PMID: 31863187 DOI: 10.1007/s00414-019-02233-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022]
Abstract
Forensic identification tests often need recourse to markers that can successfully type highly degraded DNA, and binary single nucleotide polymorphisms (SNPs) have become the variants of choice for such analyses because of their short amplified fragment lengths. The two main drawbacks of SNPs are their reduced power of discrimination per marker compared with mainstream forensic STRs and an inability to robustly detect mixed DNA-particularly using capillary electrophoresis genotyping systems such as SNaPshot™, where the dye signals are much more imbalanced than those of STR profiles. This study compiled a compact set of multiple-allele SNPs consisting of loci that had three or four nucleotide variants at the same site in order to address the lack of mixture detection capability with binary SNP tests, as well as improving levels of polymorphism per SNP by transitioning to a maximum of six or ten genotypes per locus. We report the development and optimisation of a SNaPshot-based forensic test comprising 27 tri-allelic and 2 tetra-allelic SNPs, which we named MASTiFF: a multiple-allele SNP test for forensics. Assessments of the MASTiFF panel's levels of discrimination power in the five main population groups indicate random match probabilities ranging from 10-15 down to 10-20-improving the levels possible from an equivalent number of binary SNPs. The SNaPshot test was able to detect simple mixtures successfully with more than two alleles observed in 30% of SNPs. From allele frequency data, it is estimated that more than two alleles will be present in at least one MASTiFF SNP in 99.8% of two-person mixtures, making this panel an ideal supplementary test when SNPs are chosen for the analysis of degraded forensic DNA.
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53
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Alladio E, Della Rocca C, Barni F, Dugoujon JM, Garofano P, Semino O, Berti A, Novelletto A, Vincenti M, Cruciani F. A multivariate statistical approach for the estimation of the ethnic origin of unknown genetic profiles in forensic genetics. Forensic Sci Int Genet 2019; 45:102209. [PMID: 31812099 DOI: 10.1016/j.fsigen.2019.102209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/11/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022]
Abstract
DNA typing and genetic profile data interpretation are among the most relevant topics in forensic science; among other applications, genetic profile's capability to distinguish biogeographic information about population groups, subgroups and affiliations have been largely explored in the last decade. In fact, for investigative and intelligence purposes, it is extremely useful to identify subjects and estimate their biogeographic origins by examining the recovered DNA profiles from evidence on a crime scene. Current approaches for BiogeoGraphic Ancestry (BGA) estimation using STRs profiles are usually based on Bayesian methods, which quantify the evidence in terms of likelihood ratio, supporting or not the hypothesis that a certain profile belongs to a specific ethnic group. The present study provides an alternative approach to the likelihood ratio method that involves multivariate data analysis strategies for the estimation of multiple populations. Starting from the well-known NIST US autosomal STRs dataset involving African-American, Asian, and Caucasian individuals, and moving towards further and more geographically restricted populations (such as Northern Africans vs sub-Saharan Africans, Afghans vs Iraqis and Italians vs Romanians), powerful multivariate techniques such as Sparse and Logistic Principal Component Analysis (SL-PCA), Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) and Support Vector Machines (SVM) were employed and their discriminating power was also compared. Both sPLS-DA and SVM techniques provided robust classifications, yielding high sensitivity and specificity models capable of discriminating populations on ethnic basis. This application may represent a powerful and dynamic tool for law enforcement agencies whenever a standard autosomal STR profile is obtained from the biological evidence collected at a crime scene or recovered during mass-disaster and missing person investigations.
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Affiliation(s)
- Eugenio Alladio
- Reparto CC Investigazioni Scientifiche di Roma, Sezione di Biologia, Viale Tor di Quinto 119, 00191, Roma, Italy; Dipartimento di Chimica, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy; Centro Regionale Antidoping e di Tossicologia "A. Bertinaria" di Orbassano (Torino), Regione Gonzole 10/1, 10030, Orbassano, Torino, Italy.
| | - Chiara Della Rocca
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Filippo Barni
- Reparto CC Investigazioni Scientifiche di Roma, Sezione di Biologia, Viale Tor di Quinto 119, 00191, Roma, Italy
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique (CNRS) and Université Toulouse III - Paul Sabatier, 118, route de Narbonne, 31062, Toulouse Cedex 9, France
| | - Paolo Garofano
- Centro Regionale Antidoping e di Tossicologia "A. Bertinaria" di Orbassano (Torino), Regione Gonzole 10/1, 10030, Orbassano, Torino, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università degli Studi di Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Andrea Berti
- Reparto CC Investigazioni Scientifiche di Roma, Sezione di Biologia, Viale Tor di Quinto 119, 00191, Roma, Italy
| | - Andrea Novelletto
- Dipartimento di Biologia, Università degli Studi di Roma "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Roma, Italy
| | - Marco Vincenti
- Dipartimento di Chimica, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy; Centro Regionale Antidoping e di Tossicologia "A. Bertinaria" di Orbassano (Torino), Regione Gonzole 10/1, 10030, Orbassano, Torino, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy; Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
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54
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Harthun M, Pflugbeil AM, Jede A, Schönborn H. Completion of the MIX 13 case study by evaluation of mock mixtures with the probabilistic genotyping software GenoProof® Mixture 3. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.101] [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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55
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Development of a new software for estimating credible interval of statistical indexes used for DNA evidence interpretation. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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56
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Benschop CC, van der Linden J, Hoogenboom J, Ypma R, Haned H. Automated estimation of the number of contributors in autosomal short tandem repeat profiles using a machine learning approach. Forensic Sci Int Genet 2019; 43:102150. [DOI: 10.1016/j.fsigen.2019.102150] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 01/19/2023]
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57
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Zorbo S, Jeuniaux PPJMH. DNA Recovery From Tape-Lifting Kits: Methodology and Practice. J Forensic Sci 2019; 65:641-648. [PMID: 31658369 DOI: 10.1111/1556-4029.14215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 11/28/2022]
Abstract
In the case of suspicious deaths, the technique of 1:1 taping is often used in Belgium. It consists of affixing a large number of adhesive tapes to the body of the victim. It is conventionally aimed at obtaining microtraces (e.g., fibers, hair) and is usually not used for DNA analysis. However, in some cases, DNA analysis of certain areas of interest identified on the 1:1 taping material can offer a last resort solution. The four-step method that is described in this article involves the selection of areas of interest on the body (Step 1), the selection of the corresponding tapes (Step 2), the decontamination of the tapes (Step 3), the selection of areas of interest on the tapes, for DNA sampling (Step 4). The method is illustrated by its successful application in four murder cases. In each case, DNA profiles of good quality could be identified, including profiles of persons different from the victim.
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Affiliation(s)
- Sabrina Zorbo
- National Institute of Criminalistics and Criminology (NICC-INCC), Chaussee de Vilvorde 100, Bruxelles, 1120, Belgium
| | - Patrick P J M H Jeuniaux
- National Institute of Criminalistics and Criminology (NICC-INCC), Chaussee de Vilvorde 100, Bruxelles, 1120, Belgium
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58
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Fonneløp AE, Johannessen H, Heen G, Molland K, Gill P. A retrospective study on the transfer, persistence and recovery of sperm and epithelial cells in samples collected in sexual assault casework. Forensic Sci Int Genet 2019; 43:102153. [PMID: 31505370 DOI: 10.1016/j.fsigen.2019.102153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/15/2019] [Accepted: 08/23/2019] [Indexed: 01/12/2023]
Abstract
Data from all sexual assault cases analysed at the Section of Forensic Biology at Oslo University Hospital in the period 2013-2015 were reviewed to study transfer and persistence of cells deposited on the body. Data were recorded on detection of both sperm and epithelial cells. The final dataset consist of 2141 samples from 765 cases. In this study "positive findings" refer to evidence to support the proposition that the DNA profile was contributed by the POI and do not only correspond to detection of cell type, e.g. sperm cells. Positive findings from analysis of sperm cells could be detected in samples collected up to 72 h after deposition, and was less frequently detected in oral swabs were the longest observed persistence time was 12 h. Positive findings from analysis of epithelial cells were observed up to 43 h after deposition. A high success rate was observed from penile swabs collected within 24 h of the incidence demonstrating the importance of collecting and analysing such samples in cases where no semen is detected.
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Affiliation(s)
| | | | | | | | - Peter Gill
- Oslo University Hospital, Norway; University of Oslo, Oslo, Norway
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59
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An assessment of the performance of the probabilistic genotyping software EuroForMix: Trends in likelihood ratios and analysis of Type I & II errors. Forensic Sci Int Genet 2019; 42:31-38. [DOI: 10.1016/j.fsigen.2019.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/07/2019] [Accepted: 06/07/2019] [Indexed: 01/25/2023]
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60
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Transcriptome variation in human populations and its potential application in forensics. J Appl Genet 2019; 60:319-328. [PMID: 31401728 PMCID: PMC6803616 DOI: 10.1007/s13353-019-00510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/04/2022]
Abstract
This review presents the state-of-the-art in the forensic application of genetic methods driven by the research in population transcriptomics. In the first part of the review, the constraints of using classical genomic markers are shortly reviewed. In the second part, the developments in the field of inter-population diversity at the transcriptomic level are presented. Subsequently, a potential of population-specific transcriptomic markers in forensic science applications, including ascertaining population affiliation of human samples and cell mixtures separation, are presented.
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61
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Exploring the probative value of mixed DNA profiles. Forensic Sci Int Genet 2019; 41:1-10. [DOI: 10.1016/j.fsigen.2019.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 12/19/2022]
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62
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Yang J, Lin D, Deng C, Li Z, Pu Y, Yu Y, Li K, Li D, Chen P, Chen F. The advances in DNA mixture interpretation. Forensic Sci Int 2019; 301:101-106. [PMID: 31153987 DOI: 10.1016/j.forsciint.2019.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
In forensic genetics, the analysis of DNA in biological samples is a valuable tool for personal identification. There is an increasing demand in analyzing of the mixed DNA which may provide insightful investigative instructions. With the continuous effort for the improvement of individual identification, complicated mixed stains represent a growing fraction of the samples processed by forensic laboratories. Recent technological advances have enabled quantitative analysis of DNA mixture and emerging sequencing approaches to decipher the complicated DNA mixture. Here, we describe the use of different genetic markers, typing approaches and analytical methods in mixture analysis, and how useful information can be obtained from complicated DNA mixture.
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Affiliation(s)
- Jiawen Yang
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Donghai Lin
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Chuwei Deng
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Zheng Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Yan Pu
- School of Medicine, Southeast University, Nanjing, Jiangsu 210009, PR China
| | - Yanfang Yu
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Kai Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Ding Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Peng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China.
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
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63
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Chen R, Zhao X, Ma K, Li H, Cao Y, Cao Y, Liu W. Separation of SNP profiles from DNA mixtures with two contributors via massively parallel sequencing technology. AUST J FORENSIC SCI 2019. [DOI: 10.1080/00450618.2019.1586997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ronghua Chen
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Xueying Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Ke Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yandong Cao
- Technical department, Analyses Technology Co. Ltd, Beijing, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
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64
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Asari M, Isozaki S, Hoshina C, Okuda K, Tanaka H, Horioka K, Shiono H, Shimizu K. Discrimination of haplotype in mitochondrial DNA mixtures using LNA-mediated PCR clamping. Forensic Sci Int Genet 2019; 41:58-63. [PMID: 30974414 DOI: 10.1016/j.fsigen.2019.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/20/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Locked nucleic acid (LNA) has been widely used for various genetic analyses, and has many benefits, in terms of the specificity or sensitivity of amplification, because LNA-containing primers/probes form more stable duplexes with template DNA than probes lacking LNA. Here, we developed a new method for discriminating HV1 haplotypes from mitochondrial DNA (mtDNA) mixtures by applying PCR clamping using LNA. PCR clamping is based on the selective inhibition of amplification using LNA-containing probes, which can discriminate single-nucleotide differences. Before designing probes, we selected 171 sequences with single-nucleotide variations from the HV1 region, and evaluated the specificity of LNA-containing probes for them by predicting Tm values. The differences of Tm between mismatched and exactly matched probe-template duplexes depended markedly on the type of LNA nucleotides for discriminating single-nucleotide differences, and the cytosine LNA nucleotide at the site of variations in the probes was most effective to discriminate these differences. For mixture analysis, each probe targeted one or two variations (16209C, 16217C, 16257A/16261T, 16297C/16298C, 16304C, 16362C, or 16362T) that are particularly common in the Japanese population, and seven designed probes completely inhibited the amplification of exactly matched templates. We prepared mixed samples by mixing DNA from two individuals at a ratio of 1:9, 1:4, 1:1, 4:1, or 9:1, and then performed Sanger sequencing analysis after PCR clamping with each probe. Our method distinguished each haplotype at lower ratios from two-person mixtures, and enabled sensitive detection at 12 pg of total DNA including 600 copies of mtDNA. Moreover, we analyzed three-person mixtures with representative sequences, and detected the minor haplotype of one individual present at a rate of 10% by adding two selected probes. The ability to discriminate haplotypes in mixed samples by using LNA-mediated PCR clamping indicates the potential value of mtDNA analysis in criminal investigations.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan.
| | - Shotaro Isozaki
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Chisato Hoshina
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Katsuhiro Okuda
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Hiroki Tanaka
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Kie Horioka
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Hiroshi Shiono
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Keiko Shimizu
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
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65
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Gosch A, Courts C. On DNA transfer: The lack and difficulty of systematic research and how to do it better. Forensic Sci Int Genet 2019; 40:24-36. [PMID: 30731249 DOI: 10.1016/j.fsigen.2019.01.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/21/2018] [Accepted: 01/30/2019] [Indexed: 01/07/2023]
Abstract
Since DNA from touched items and surfaces ("touch DNA") can successfully and reliably be analyzed, the question as to how a particular DNA containing sample came to be from where it was recovered is of increasing forensic interest and expert witnesses in court are increasingly challenged to assess for instance whether an incriminatory DNA sample matching to a suspect could have been transferred to the crime scene in an innocent manner and to guess at the probability of such an occurrence. The latter however will frequently entail expressing a subjective probability i.e. simply making a best guess from experience. There is, to the present date, an extensive and complex body of literature on primary, secondary, tertiary and even higher order DNA transfer, its possibility, plausibility, dependency on an array of variables and factors and vast numbers of permutations thereof. However, from our point of view there is a lack of systematic data on DNA transfer with existing research widely varying in quality and relevance. Our aim was, starting from a comprehensive survey of the status quo and appreciating its increasing importance, to in the first part of our review raise consciousness towards the underestimated and insufficiently accounted for complexity of DNA transfer and thus appendant research of forensic scientists serving as expert witnesses in court but also acting in the role of a journal referee to point them to areas of criticism when reviewing a manuscript on DNA transfer. In the second part, we present propositions how to systematize and integrate future research efforts concerning DNA transfer. Also, we present a searchable database providing an extensive overview of the current state of knowledge on DNA transfer, intended to facilitate the identification of relevant studies adding knowledge to a specific question and thus help forensic experts to base their opinion on a broader, more complete and more reproducible selection of studies.
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Affiliation(s)
- Annica Gosch
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Arnold-Heller-Strasse 12, 24105 Kiel, Germany
| | - Cornelius Courts
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Arnold-Heller-Strasse 12, 24105 Kiel, Germany.
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66
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Young BA, Gettings KB, McCord B, Vallone PM. Estimating number of contributors in massively parallel sequencing data of STR loci. Forensic Sci Int Genet 2019; 38:15-22. [DOI: 10.1016/j.fsigen.2018.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/12/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
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67
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Deconvolution of blood-blood mixtures using DEPArrayTM separated single cell STR profiling. Rechtsmedizin (Berl) 2018. [DOI: 10.1007/s00194-018-0291-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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68
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Four model variants within a continuous forensic DNA mixture interpretation framework: Effects on evidential inference and reporting. PLoS One 2018; 13:e0207599. [PMID: 30458020 PMCID: PMC6245789 DOI: 10.1371/journal.pone.0207599] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/13/2018] [Indexed: 12/11/2022] Open
Abstract
Continuous mixture interpretation methods that employ probabilistic genotyping to compute the Likelihood Ratio (LR) utilize more information than threshold-based systems. The continuous interpretation schemes described in the literature, however, do not all use the same underlying probabilistic model and standards outlining which probabilistic models may or may not be implemented into casework do not exist; thus, it is the individual forensic laboratory or expert that decides which model and corresponding software program to implement. For countries, such as the United States, with an adversarial legal system, one can envision a scenario where two probabilistic models are used to present the weight of evidence, and two LRs are presented by two experts. Conversely, if no independent review of the evidence is requested, one expert using one model may present one LR as there is no standard or guideline requiring the uncertainty in the LR estimate be presented. The choice of model determines the underlying probability calculation, and changes to it can result in non-negligible differences in the reported LR or corresponding verbal categorization presented to the trier-of-fact. In this paper, we study the impact of model differences on the LR and on the corresponding verbal expression computed using four variants of a continuous mixture interpretation method. The four models were tested five times each on 101, 1-, 2- and 3-person experimental samples with known contributors. For each sample, LRs were computed using the known contributor as the person of interest. In all four models, intra-model variability increased with an increase in the number of contributors and with a decrease in the contributor’s template mass. Inter-model variability in the associated verbal expression of the LR was observed in 32 of the 195 LRs used for comparison. Moreover, in 11 of these profiles there was a change from LR > 1 to LR < 1. These results indicate that modifications to existing continuous models do have the potential to significantly impact the final statistic, justifying the continuation of broad-based, large-scale, independent studies to quantify the limits of reliability and variability of existing forensically relevant systems.
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69
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Buckleton JS, Bright JA, Cheng K, Budowle B, Coble MD. NIST interlaboratory studies involving DNA mixtures (MIX13): A modern analysis. Forensic Sci Int Genet 2018; 37:172-179. [DOI: 10.1016/j.fsigen.2018.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 11/30/2022]
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70
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Pilli E, Boccone S, Agostino A, Virgili A, D'Errico G, Lari M, Rapone C, Barni F, Moggi Cecchi J, Berti A, Caramelli D. From unknown to known: Identification of the remains at the mausoleum of fosse Ardeatine. Sci Justice 2018; 58:469-478. [DOI: 10.1016/j.scijus.2018.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/08/2018] [Accepted: 05/20/2018] [Indexed: 11/26/2022]
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71
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Determination of the possible number of genotypes which can contribute to DNA mixtures: Non-computer assisted deconvolution should not be attempted for greater than two person mixtures. Forensic Sci Int Genet 2018; 37:235-240. [DOI: 10.1016/j.fsigen.2018.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 08/05/2018] [Accepted: 09/05/2018] [Indexed: 11/20/2022]
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72
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NIST interlaboratory studies involving DNA mixtures (MIX05 and MIX13): Variation observed and lessons learned. Forensic Sci Int Genet 2018; 37:81-94. [DOI: 10.1016/j.fsigen.2018.07.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/24/2018] [Accepted: 07/31/2018] [Indexed: 11/19/2022]
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73
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Kokshoorn B, Aarts LHJ, Ansell R, Connolly E, Drotz W, Kloosterman AD, McKenna LG, Szkuta B, van Oorschot RAH. Sharing data on DNA transfer, persistence, prevalence and recovery: Arguments for harmonization and standardization. Forensic Sci Int Genet 2018; 37:260-269. [PMID: 30273824 DOI: 10.1016/j.fsigen.2018.09.006] [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: 07/31/2018] [Revised: 08/31/2018] [Accepted: 09/19/2018] [Indexed: 12/01/2022]
Abstract
Sharing data between forensic scientists on DNA transfer, persistence, prevalence and recovery (TPPR) is crucial to advance the understanding of these issues in the criminal justice community. We present the results of a collaborative exercise on reporting forensic genetics findings given activity level propositions. This exercise outlined differences in the methodology that was applied by the participating laboratories, as well as limitations to the use of published data on DNA TPPR. We demonstrate how publication of experimental results in scientific journals can be further improved to allow for an adequate use of these data. Steps that can be taken to share and use these data for research and casework purposes are outlined, and the prospects for future sharing of data through publicly accessible databases are discussed. This paper also explores potential avenues to proceed with implementation and is intended to fuel the discussion on sharing data pertaining to DNA TPPR issues. It is further suggested that international standardization and harmonization on these topics will benefit the forensic DNA community as it has been achieved in the past with the harmonization of STR typing systems.
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Affiliation(s)
- Bas Kokshoorn
- Division Biological Traces, Netherlands Forensic Institute, P.O. Box 24044 2490 AA, The Hague, the Netherlands.
| | - Lambertus H J Aarts
- Division Biological Traces, Netherlands Forensic Institute, P.O. Box 24044 2490 AA, The Hague, the Netherlands
| | - Ricky Ansell
- Swedish National Forensic Centre, SE-581 94, Linköping, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83, Linköping, Sweden
| | - Edward Connolly
- Forensic Science Ireland, Garda HQ, Phoenix Park, Dublin 8, Ireland
| | - Weine Drotz
- Swedish National Forensic Centre, SE-581 94, Linköping, Sweden
| | - Ate D Kloosterman
- Division Biological Traces, Netherlands Forensic Institute, P.O. Box 24044 2490 AA, The Hague, the Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE, Amsterdam, the Netherlands
| | - Louise G McKenna
- Forensic Science Ireland, Garda HQ, Phoenix Park, Dublin 8, Ireland
| | - Bianca Szkuta
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, 31 Forensic Drive, Macleod, Vic, 3085, Australia; School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, Vic, 3220, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, 31 Forensic Drive, Macleod, Vic, 3085, Australia; School of Molecular Sciences, La Trobe University, Bundoora, Vic, 3086, Australia
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74
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Evaluation of forensic genetics findings given activity level propositions: A review. Forensic Sci Int Genet 2018; 36:34-49. [DOI: 10.1016/j.fsigen.2018.06.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 12/31/2022]
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75
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Whose blood is it? Application of DEPArray™ technology for the identification of individual/s who contributed blood to a mixed stain. Int J Legal Med 2018; 133:419-426. [DOI: 10.1007/s00414-018-1912-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 08/13/2018] [Indexed: 11/25/2022]
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76
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Gill P, Hicks T, Butler JM, Connolly E, Gusmão L, Kokshoorn B, Morling N, van Oorschot RAH, Parson W, Prinz M, Schneider PM, Sijen T, Taylor D. DNA commission of the International society for forensic genetics: Assessing the value of forensic biological evidence - Guidelines highlighting the importance of propositions: Part I: evaluation of DNA profiling comparisons given (sub-) source propositions. Forensic Sci Int Genet 2018; 36:189-202. [PMID: 30041098 DOI: 10.1016/j.fsigen.2018.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/02/2018] [Indexed: 01/23/2023]
Abstract
The interpretation of evidence continues to be one of the biggest challenges facing the forensic community. This is the first of two papers intended to provide advice on difficult aspects of evaluation and in particular on the formulation of propositions. The scientist has a dual role: investigator (crime-focused), where often there is no suspect available and a database search may be required; evaluator (suspect-focused), where the strength of evidence is assessed in the context of the case. In investigative mode, generally the aim is to produce leads regarding the source of the DNA. Sub-source level propositions will be adequate to help identify potential suspects who can be further investigated by the authorities. Once in evaluative mode, given the defence version of events of the person of interest, it may become necessary to consider alternatives that go beyond the source of the DNA (i.e., to consider activity level propositions). In the evaluation phase, it is crucial that formulation of propositions allows the assessment of all the results that will help with the issue at hand. Propositions should therefore be precise (indication of the number of contributors, information on the relevant population etc.), be about causes, not effects (e.g. a 'matching' DNA profile) and to avoid bias, must not be findings-led. This means that ideally, propositions should be decided based on the case information and before the results of the comparisons are known. This paper primarily reflects upon what has been coined as "sub-source level propositions". These are restricted to the evaluation of the DNA profiles themselves, and help answer the issue regarding the source of the DNA. It is to be emphasised that likelihood ratios given sub-source level propositions cannot be carried over to a different level - for example, activity level propositions, where the DNA evidence is put into the context of the alleged activities. This would be highly misleading and could give rise to miscarriages of justice; this will be discussed in a second paper. The value of forensic results depends not only on propositions, but also on the type of results (e.g. allelic designations, peak heights, replicates) and upon the model used: it is therefore important to discuss these aspects. Finally, since communication is key to help understanding by courts, we will explore how to convey the value of the results and explain the importance of avoiding the practice of transposing the conditional.
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Affiliation(s)
- Peter Gill
- Oslo University Hospital, Oslo, Norway; University of Oslo, Oslo, Norway.
| | - Tacha Hicks
- Faculty of Law, Criminal Justice and Public Administration, School of Criminal Justice, University of Lausanne, Lausanne, Switzerland; Fondation pour la formation continue Universitaire Lausannoise (UNIL-EPFL), 1015 Dorigny, Switzerland.
| | - John M Butler
- National Institute of Standards and Technology, Special Programs Office, Gaithersburg, MD, USA
| | - Ed Connolly
- Forensic Science Ireland, Garda HQ, Phoenix Park, Dublin 8, D08 HN3X, Ireland
| | - Leonor Gusmão
- State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Portugal; Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal
| | - Bas Kokshoorn
- Netherlands Forensic Institute, Division Biological Traces, P.O. Box 24044, 2490 AA The Hague, The Netherlands
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Service Centre, Macleod, VIC 3085, Australia; School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | | | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Titia Sijen
- Netherlands Forensic Institute, Division Biological Traces, P.O. Box 24044, 2490 AA The Hague, The Netherlands
| | - Duncan Taylor
- Forensic Science South Australia, 21 Divett Place, Adelaide, SA 5000, Australia; School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
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77
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Barrio P, Crespillo M, Luque J, Aler M, Baeza-Richer C, Baldassarri L, Carnevali E, Coufalova P, Flores I, García O, García M, González R, Hernández A, Inglés V, Luque G, Mosquera-Miguel A, Pedrosa S, Pontes M, Porto M, Posada Y, Ramella M, Ribeiro T, Riego E, Sala A, Saragoni V, Serrano A, Vannelli S. GHEP-ISFG collaborative exercise on mixture profiles (GHEP-MIX06). Reporting conclusions: Results and evaluation. Forensic Sci Int Genet 2018; 35:156-163. [DOI: 10.1016/j.fsigen.2018.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/30/2018] [Accepted: 05/13/2018] [Indexed: 11/25/2022]
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78
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Kalafut T, Schuerman C, Sutton J, Faris T, Armogida L, Bright JA, Buckleton J, Taylor D. Implementation and validation of an improved allele specific stutter filtering method for electropherogram interpretation. Forensic Sci Int Genet 2018; 35:50-56. [DOI: 10.1016/j.fsigen.2018.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 11/26/2022]
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79
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Gittelson S, Berger CEH, Jackson G, Evett IW, Champod C, Robertson B, Curran JM, Taylor D, Weir BS, Coble MD, Buckleton JS. A response to "Likelihood ratio as weight of evidence: A closer look" by Lund and Iyer. Forensic Sci Int 2018; 288:e15-e19. [PMID: 29857959 PMCID: PMC7306225 DOI: 10.1016/j.forsciint.2018.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/15/2018] [Indexed: 11/24/2022]
Abstract
Recently, Lund and Iyer (L&I) raised an argument regarding the use of likelihood ratios in court. In our view, their argument is based on a lack of understanding of the paradigm. L&I argue that the decision maker should not accept the expert's likelihood ratio without further consideration. This is agreed by all parties. In normal practice, there is often considerable and proper exploration in court of the basis for any probabilistic statement. We conclude that L&I argue against a practice that does not exist and which no one advocates. Further we conclude that the most informative summary of evidential weight is the likelihood ratio. We state that this is the summary that should be presented to a court in every scientific assessment of evidential weight with supporting information about how it was constructed and on what it was based.
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Affiliation(s)
- Simone Gittelson
- Centre for Forensic Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia.
| | - Charles E H Berger
- Leiden University, Institute for Criminal Law and Criminology, P.O. Box 9520, 2300 RA Leiden, The Netherlands
| | - Graham Jackson
- Advance Forensic Science, St. Andrews, Scotland, UK; School of Science, Engineering and Technology, Abertay University, Dundee, Scotland, UK
| | - Ian W Evett
- Principal Forensic Services Ltd., 34 Southborough Road, Bickley, Bromley, Kent BR1 2EB, UK
| | - Christophe Champod
- Ecole des Sciences Criminelles, Faculty of Law, Criminal Justice and Public Administration, Université de Lausanne, Batochime - Quartier Sorge, CH-1015 Lausanne-Dorigny, Switzerland
| | | | - James M Curran
- Department of Statistics, University of Auckland, PB 92019, Auckland, New Zealand
| | - Duncan Taylor
- Forensic Science South Australia, 21 Divett Place, Adelaide, SA 5000, Australia; School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Bruce S Weir
- University of Washington, Department of Biostatistics, Seattle, WA 98195, United States
| | - Michael D Coble
- National Institute of Standards and Technology, Applied Genetics Group, 100 Bureau Drive, Gaithersburg, MD 20899, United States; Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, United States
| | - John S Buckleton
- University of Washington, Department of Biostatistics, Seattle, WA 98195, United States; Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
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80
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Hessab T, Aranha RS, Moura-Neto RS, Balding DJ, Schrago CG. Evaluating DNA evidence in a genetically complex population. Forensic Sci Int Genet 2018; 36:141-147. [PMID: 29990826 DOI: 10.1016/j.fsigen.2018.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/28/2022]
Abstract
In forensic genetics, the likelihood ratio (LR), measuring the value of DNA profile evidence, is computed from a database of allele frequencies. Here, we address the choice of database and adjustments for population structure and sample size in the context of Brazil. The Brazilian population underwent a complex process of colonization, migration and mating, which created an admixed genetic composition that makes it difficult to obtain an appropriate database for a given case. National databases are now available, as well as databases for many Brazilian states. However, those databases are not statistically random samples, and state boundaries may not accurately reflect the sub-structuring of genetic diversity. We compared the LR calculated using the relevant state-specific database with the statistics calculated when a national database and when international databases were used. We evaluated two methods of adjustment for population structure, due to Wright [13] and Balding and Nichols [14]. We also considered two adjustments for database sample size: the Balding size bias correction [15] and a minimum allele frequency [16]. Our results show that the use of a national database with the Balding and Nichols adjustment and θ = 0.002 generated lower LR values than did the state-specific database in more than 50% of the profiles simulated using the state-based allele frequencies, while θ = 0.01 produced lower LRs for more than 90% of the profiles. We conclude that the utilization of a national database for Brazilian cases can be justified in association with the appropriate adjustment for population structure.
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Affiliation(s)
- T Hessab
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Instituto de Pesquisa e Perícias em Genética Forense, DGPTC/PCERJ, Rio de Janeiro, RJ, Brazil.
| | - R S Aranha
- Escola de Matemática Aplicada, Fundação Getúlio Vargas, Rio de Janeiro, RJ, Brazil
| | - R S Moura-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - D J Balding
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics & Statistics, The University of Melbourne, Melbourne, Australia
| | - C G Schrago
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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81
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Tao R, Wang S, Zhang J, Zhang J, Yang Z, Sheng X, Hou Y, Zhang S, Li C. Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review). Int J Legal Med 2018; 132:1247-1261. [PMID: 29802461 DOI: 10.1007/s00414-018-1862-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/11/2018] [Indexed: 02/08/2023]
Abstract
Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.
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Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Xiang Sheng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China. .,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
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82
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Contributors are a nuisance (parameter) for DNA mixture evidence evaluation. Forensic Sci Int Genet 2018; 37:116-125. [PMID: 30145539 DOI: 10.1016/j.fsigen.2018.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/07/2018] [Accepted: 05/11/2018] [Indexed: 11/23/2022]
Abstract
Recently, a debate has arisen around the number of contributors postulated in hypotheses for the purpose of weight of evidence calculations on DNA mixture profiles. Specifically the issue at stake is whether or not one should have the same number of contributors under both hypotheses for which a likelihood ratio is calculated. In this paper we aim to clarify this issue. We take the general approach of considering the number of contributors as a nuisance parameter. Two central assumptions then determine the form of the overall likelihood ratio: whether the prior distributions of the nuisance parameter are equivalent given both hypotheses and whether they depend on the hypotheses. Examples are given for both scenarios where we have either independence or strong dependence between the prior distributions of the number of contributors and the hypotheses. Moreover, examples for different kinship scenarios are presented. In conclusion, the overall likelihood ratio does not only depend on likelihood ratios for fixed values of the nuisance parameter but may also vary considerably with different prior distributions.
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83
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He H, Zha L, Cai J, Huang J. The forensic value of X-linked markers in mixed-male DNA analysis. Int J Legal Med 2018; 132:1281-1285. [PMID: 29728767 DOI: 10.1007/s00414-018-1841-5] [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: 01/14/2018] [Accepted: 04/03/2018] [Indexed: 11/28/2022]
Abstract
Autosomal genetic markers and Y chromosome markers have been widely applied in analysis of mixed stains at crime scenes by forensic scientists. However, true genotype combinations are often difficult to distinguish using autosomal markers when similar amounts of DNA are contributed by multiple donors. In addition, specific individuals cannot be determined by Y chromosomal markers because male relatives share the same Y chromosome. X-linked markers, possessing characteristics somewhere intermediate between autosomes and the Y chromosome, are less universally applied in criminal casework. In this paper, X markers are proposed to apply to male mixtures because their true genes can be more easily and accurately recognized than the decision of the genotypes of AS markers. In this study, an actual two-man mixed stain from a forensic case file and simulated male-mixed DNA were examined simultaneously with the X markers and autosomal markers. Finally, the actual mixture was separated successfully by the X markers, although it was unresolved by AS-STRs, and the separation ratio of the simulated mixture was much higher using Chr X tools than with AS methods. We believe X-linked markers provide significant advantages in individual discrimination of male mixtures that should be further applied to forensic work.
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Affiliation(s)
- HaiJun He
- Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shanxi Province, People's Republic of China.,Criminal Investigation Division, Changsha Public Security Bureaus, Changsha, 410004, Hunan, People's Republic of China
| | - Lagabaiyila Zha
- Department of Forensic Sciences, School of Basic Medicine, Central South University, Changsha, Hunan, People's Republic of China
| | - JinHong Cai
- Department of Forensic Genetics, Brain Hospital of Hunan Province, Hunan University of Chinese Medicine, Changsha, 410007, People's Republic of China
| | - Jian Huang
- Department of Forensic Genetics, Brain Hospital of Hunan Province, Hunan University of Chinese Medicine, Changsha, 410007, People's Republic of China.
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84
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Zander J, Otremba P, Nagy M. Validation of haplotype-specific extraction for separating a mitochondrial DNA model mixture and application to simulated casework. Forensic Sci Int Genet 2018; 35:57-64. [PMID: 29665468 DOI: 10.1016/j.fsigen.2018.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 01/14/2023]
Abstract
Haplotype-specific extraction (HSE) is a new field of application for the separation of mitochondrial DNA (mtDNA) mixtures and is developed to identify the mtDNA haplotypes of the contributors subsequently by sequencing. Here we show the validation of HSE with an exemplary mitochondrial DNA mixture into its individual haplotypes according to our laboratory standards. These specify several critical areas of assay performance to be tested, such as sensitivity, robustness and mixture studies comprising varying proportions of their components,degraded samples and samples of different qualities and material. Wereport the successful and unambiguous analysis of the exemplary separated mitochondrial DNA mixture under various conditions as well as simulated casework samples, which manifest as mixed nucleotide calls at single base positions previously. Here we demonstrate that the HSE assay is high sensitive, stable against degradation and applicable in a wide range of sample qualities. Based on our findings from the validation study, we believe that this assay has great potential power and may be useful for distinguishing among the mtDNA of individuals and their geographical origin in mixed DNA samples.
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Affiliation(s)
- Judith Zander
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
| | - Petra Otremba
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
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85
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Hussing C, Huber C, Bytyci R, Mogensen HS, Morling N, Børsting C. Sequencing of 231 forensic genetic markers using the MiSeq FGx™ forensic genomics system - an evaluation of the assay and software. Forensic Sci Res 2018; 3:111-123. [PMID: 30483659 PMCID: PMC6197110 DOI: 10.1080/20961790.2018.1446672] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/26/2018] [Indexed: 02/07/2023] Open
Abstract
The MiSeq FGx™ Forensic Genomics System types 231 genetic markers in one multiplex polymerase chain reaction (PCR) assay. The markers include core forensic short tandem repeats (STRs) as well as identity, ancestry and phenotype informative short nucleotide polymorphisms (SNPs). In this work, the MiSeq FGx™ Forensic Genomics System was evaluated by analysing reproducibility, sensitivity, mixture identification and forensic phenotyping capabilities of the assay. Furthermore, the genotype calling of the ForenSeq™ Universal Analysis Software was verified by analysing fastq.gz files from the MiSeq FGx™ platform using the softwares STRinNGS and GATK. Overall, the performance of the MiSeq FGx™ Forensic Genomics System was high. However, locus and allele drop-outs were relatively frequent at six loci (two STRs and four human identification SNPs) due to low read depth or skewed heterozygote balances, and the stutter ratios were larger than those observed with conventional STR genotyping methods. The risk of locus and allele drop-outs increased dramatically when the amount of DNA in the first PCR was lower than 250 pg. Two-person 50:1 mixtures were identified as mixtures, whereas 100:1 and 1 000:1 mixtures were not. Y-chromosomal short tandem repeats (Y-STRs) alleles were detected in the 100:1 and 1 000:1 female/male mixtures. The ForenSeq™ Universal Analysis Software provided the data analyst with useful alerts that simplified the analysis of the large number of markers. Many of the alerts were due to user-defined, locus-specific criteria. The results shown here indicated that the default settings should be altered for some loci. Also, recommended changes to the assay and software are discussed.
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Affiliation(s)
- Christian Hussing
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christina Huber
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajmonda Bytyci
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helle S Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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86
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Ciavaglia S, Linacre A. OzPythonPlex: An optimised forensic STR multiplex assay set for the Australasian carpet python (Morelia spilota). Forensic Sci Int Genet 2018; 34:231-248. [PMID: 29571024 DOI: 10.1016/j.fsigen.2018.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/24/2018] [Accepted: 03/01/2018] [Indexed: 12/12/2022]
Abstract
Reptile species, and in particular snakes, are protected by national and international agreements yet are commonly handled illegally. To aid in the enforcement of such legislation, we report on the development of three 11-plex assays from the genome of the carpet python to type 24 loci of tetra-nucleotide and penta-nucleotide repeat motifs (pure, compound and complex included). The loci range in size between 70 and 550 bp. Seventeen of the loci are newly characterised with the inclusion of seven previously developed loci to facilitate cross-comparison with previous carpet python genotyping studies. Assays were optimised in accordance with human forensic profiling kits using one nanogram template DNA. Three loci are included in all three of the multiplex reactions as quality assurance markers, to ensure sample identity and genotyping accuracy is maintained across the three profiling assays. Allelic ladders have been developed for the three assays to ensure consistent and precise allele designation. A DNA reference database of allele frequencies is presented based on 249 samples collected from throughout the species native range. A small number of validation tests are conducted to demonstrate the utility of these multiplex assays. We suggest further appropriate validation tests that should be conducted prior to the application of the multiplex assays in criminal investigations involving carpet pythons.
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Affiliation(s)
- Sherryn Ciavaglia
- Science and Advice for Scottish Agriculture, Edinburgh, United Kingdom; College of Science & Engineering, Flinders University, Adelaide, Australia.
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, Australia
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87
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Mo SK, Ren ZL, Yang YR, Liu YC, Zhang JJ, Wu HJ, Li Z, Bo XC, Wang SQ, Yan JW, Ni M. A 472-SNP panel for pairwise kinship testing of second-degree relatives. Forensic Sci Int Genet 2018; 34:178-185. [PMID: 29510334 DOI: 10.1016/j.fsigen.2018.02.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/22/2018] [Accepted: 02/25/2018] [Indexed: 10/17/2022]
Abstract
Kinship testing based on genetic markers, as forensic short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), has valuable practical applications. Paternity and first-degree relationship can be accurately identified by current commonly-used forensic STRs and reported SNP markers. However, second-degree and more distant relationships remain challenging. Although ∼105-106 SNPs can be used to estimate relatedness of higher degrees, genome-wide genotyping and analysis may be impractical for forensic use. With rapid growth of human genome data sets, it is worthwhile to explore additional markers, especially SNPs, for kinship analysis. Here, we reported an autosomal SNP panel consisted of 342 SNP selected from >84 million SNPs and 131 SNPs from previous systems. We genotyped these SNPs in 136 Chinese individuals by multiplex amplicon Massively Parallel Sequencing, and performed pairwise gender-independent kinship testing. The specificity and sensitivity of these SNPs to distinguish second-degree relatives and the unrelated was 99.9% and 100%, respectively, compared with 53.7% and 99.9% of 19 commonly-used forensic STRs. Moreover, the specificity increased to 100% by the combined use of these STRs and SNPs. The 472-SNP panel could also greatly facilitate the discrimination among different relationships. We estimated that the power of ∼6.45 SNPs were equivalent to one forensic STR in the scenario of 2nd-degree relative pedigree. Altogether, we proposed a panel of 472 SNP markers for kinship analysis, which could be important supplementary of current forensic STRs to solve the problem of second-degree relative testing.
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Affiliation(s)
- Shao-Kang Mo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China; Department of Reproductive Center, General Hospital of Lanzhou Military Region, Lanzhou 730050, China.
| | - Zi-Lin Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Ya-Ran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ya-Cheng Liu
- Department of Genetics, Beijing Tongda Shoucheng Institute of Forensic Science, Beijing 100192, China.
| | - Jing-Jing Zhang
- Department of Biotechnology, Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Hui-Juan Wu
- Department of Biotechnology, Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Zhen Li
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Xiao-Chen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Sheng-Qi Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Jiang-Wei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ming Ni
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
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88
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Weight of the evidence of genetic investigations of ancestry informative markers. Theor Popul Biol 2018; 120:1-10. [DOI: 10.1016/j.tpb.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 01/03/2023]
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89
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Estimation of the number of contributors of theoretical mixture profiles based on allele counting: Does increasing the number of loci increase success rate of estimates? Forensic Sci Int Genet 2018; 33:24-32. [DOI: 10.1016/j.fsigen.2017.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/06/2017] [Accepted: 11/12/2017] [Indexed: 11/22/2022]
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90
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A retrospective study of sexual offences in Zambia. J Forensic Leg Med 2018; 54:23-33. [PMID: 29306795 DOI: 10.1016/j.jflm.2017.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 11/24/2022]
Abstract
Zambia has recently reported high incidences of sexual abuse against women and children. Zambian law categorises sexual offences into rape, defilement, incest and others, with defilement constituting the majority of the reported cases (>89%). Between 2010 and 2012, convictions of defilement cases were achieved in only 13% of cases reported to the police. DNA evidence has shown prominence in resolving crimes, specifically as an identification tool in sexual offences. Currently there is no empirical evidence describing the role of forensic evidence in sexual crimes in Zambia; as such a retrospective study was conducted to evaluate this between 2007 and 2014 (n = 1154). Only 14 (0.1%) of the cases had forensic samples collected in the form of a vaginal swab for semen analysis. In all cases where a suspect was identified (60%), identification was based on the witness/victim testimonies, and in no case, was forensic DNA evidence used to assist in identification or corroborate the testimonies. Overall, 28.1% of cases were taken to court and the conviction rate was 12.4%. These findings support the use of employing DNA evidence in sexual offence cases to aid the identification of suspects, which is hypothesised to increase the number of cases prosecuted in Zambia.
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91
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Marquis R, Cadola L, Mazzella WD, Hicks T. What is the error margin of your signature analysis? Forensic Sci Int 2017; 281:e1-e8. [DOI: 10.1016/j.forsciint.2017.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/31/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
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92
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Götz FM, Schönborn H, Borsdorf V, Pflugbeil AM, Labudde D. GenoProof Mixture 3—New software and process to resolve complex DNA mixtures. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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93
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Manabe S, Morimoto C, Hamano Y, Fujimoto S, Tamaki K. Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model. PLoS One 2017; 12:e0188183. [PMID: 29149210 PMCID: PMC5693437 DOI: 10.1371/journal.pone.0188183] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/02/2017] [Indexed: 02/01/2023] Open
Abstract
In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI) from these samples are challenging. In this study, we developed a new open-source software “Kongoh” for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1–4 persons’ contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR) of a POI’s contribution in true contributors and non-contributors by using 2–4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI’s contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples.
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Affiliation(s)
- Sho Manabe
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chie Morimoto
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuya Hamano
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Forensic Science Laboratory, Kyoto Prefectural Police Headquarters, Kyoto, Japan
| | - Shuntaro Fujimoto
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- * E-mail:
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94
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Zhang P, Zhu Y, Li Y, Zhu S, Ma R, Zhao M, Li J. Forensic evaluation of STR typing reliability in lung cancer. Leg Med (Tokyo) 2017; 30:38-41. [PMID: 29154002 DOI: 10.1016/j.legalmed.2017.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/26/2017] [Accepted: 11/10/2017] [Indexed: 01/07/2023]
Abstract
Short tandem repeats (STR) analysis is the gold standard method in the forensics field for personal identification and paternity testing. In cancerous tissues, STR markers are gaining attention, with some studies showing increased instability. Lung cancer, which is one of the most commonmalignancies, has become the most lethal among all cancers. In certain situations, lung cancer tissues may be the only resource available for forensic analysis. Therefore, evaluating the reliability of STR markers in lung cancer tissues is required to avoid false exclusions. In this study, 75 lung cancer tissue samples were examined to evaluate the reliability of various STR markers. Out of the 75 examined samples, 24 of the cancerous samples (32%) showed genetic alterations on at least one STR loci, totaling 55 times. The most common type of STR variation was a partial loss of heterozygosity, with the D5S818 loci having the highest variation frequency and no alterations detected on the D2S441 and Penta E loci. Moreover, STR variation frequencies were shown to increase with an increased patient age and increased clinical and pathological characteristics, thus an older patient with an advanced stage of progression exhibited a higher variation frequency. Overall, this study provides forensic scientists with further insight into STR analysis relating to lung cancer tissue.
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Affiliation(s)
- Peng Zhang
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Ying Zhu
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yongguo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing 400016, China
| | - Shisheng Zhu
- Faculty of Medical Technology, Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Ruoxiang Ma
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing 400016, China
| | - Minzhu Zhao
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing 400016, China
| | - Jianbo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China.
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95
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The paradigm shift in DNA profile interpretation. Forensic Sci Int Genet 2017; 31:e24-e32. [DOI: 10.1016/j.fsigen.2017.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/04/2017] [Indexed: 11/21/2022]
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96
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Tan Y, Wang L, Wang H, Tian H, Li Z, Wang Q, Jian H, Cao S, Liang W, Zhang L. An investigation of a set of DIP-STR markers to detect unbalanced DNA mixtures among the southwest Chinese Han population. Forensic Sci Int Genet 2017; 31:34-39. [PMID: 28826062 DOI: 10.1016/j.fsigen.2017.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/09/2017] [Accepted: 08/11/2017] [Indexed: 11/19/2022]
Abstract
The resolution of DNA mixtures is still a difficult problem that is worthy of further study. A common method applied for analysing mixtures is the use of autosomal STR markers as well as related calculation software based on genotypes; however, these markers have a limitation in detecting minor DNA in unbalanced mixtures if major DNA constitutes over 95% of the stain. Novel biomarkers, such as Y-STR, DIP-STR and SNP-STR, have been shown to perform well in distinguishing DNA donors in this type of mixture. DIP-STR can successfully target minor DNA in 1000-fold background DNA using two separate allele-specific primers. However, whether this method can successfully detect minor DNA primarily depends on the distribution of the DIPs in a population. Until now, only Swiss population data have been reported; therefore in this study, we selected 10 DIP-STR markers that performed well in the Swiss population and investigated whether these markers were also useful among the southwest Chinese Han population. The allele frequencies were estimated based on 152 samples, and six of the ten DIP-STR makers had a relatively high probability of informative markers (I value), which indicated their potential usefulness in the southwest Chinese Han population. A comparative study of DIP-STR markers and autosomal STR markers demonstrated that DIP-STR markers detected minor DNA at a ratio of 1:1000, while autosomal STR markers often failed to genotype minor DNA because of strong background noises caused by large amount of major DNA. However, the discrimination power was not high enough using these six DIPs alone. Therefore, we suggest that development of a panel with more loci is imperative and that a panel combined with DIP-STR and SNP-STR markers may be a possible way to achieve better discrimination power.
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Affiliation(s)
- Yu Tan
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Li Wang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Hui Wang
- Institute of Forensic Science, Chengdu Public Security Bureau,Chengdu, 610081, Sichuan, China
| | - Huan Tian
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zhilong Li
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qian Wang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Hui Jian
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Shuqiang Cao
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
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97
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Fonneløp AE, Ramse M, Egeland T, Gill P. The implications of shedder status and background DNA on direct and secondary transfer in an attack scenario. Forensic Sci Int Genet 2017; 29:48-60. [DOI: 10.1016/j.fsigen.2017.03.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/15/2017] [Accepted: 03/18/2017] [Indexed: 11/27/2022]
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98
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Vohr SH, Gordon R, Eizenga JM, Erlich HA, Calloway CD, Green RE. A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures. Forensic Sci Int Genet 2017; 30:93-105. [PMID: 28667863 DOI: 10.1016/j.fsigen.2017.05.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/05/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022]
Abstract
Massively parallel (next-generation) sequencing provides a powerful method to analyze DNA from many different sources, including degraded and trace samples. A common challenge, however, is that many forensic samples are often known or suspected mixtures of DNA from multiple individuals. Haploid lineage markers, such as mitochondrial (mt) DNA, are useful for analysis of mixtures because, unlike nuclear genetic markers, each individual contributes a single sequence to the mixture. Deconvolution of these mixtures into the constituent mitochondrial haplotypes is challenging as typical sequence read lengths are too short to reconstruct the distinct haplotypes completely. We present a powerful computational approach for determining the constituent haplotypes in massively parallel sequencing data from potentially mixed samples. At the heart of our approach is an expectation maximization based algorithm that co-estimates the overall mixture proportions and the source haplogroup for each read individually. This approach, implemented in the software package mixemt, correctly identifies haplogroups from mixed samples across a range of mixture proportions. Furthermore, our method can separate fragments in a mixed sample by the most likely originating contributor and generate reconstructions of the constituent haplotypes based on known patterns of mtDNA diversity.
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Affiliation(s)
- Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA.
| | - Rachel Gordon
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
| | - Jordan M Eizenga
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Henry A Erlich
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
| | - Cassandra D Calloway
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA; Forensic Science Graduate Program, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
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99
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Oldoni F, Castella V, Grosjean F, Hall D. Sensitive DIP-STR markers for the analysis of unbalanced mixtures from “touch” DNA samples. Forensic Sci Int Genet 2017; 28:111-117. [DOI: 10.1016/j.fsigen.2017.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/27/2017] [Accepted: 02/09/2017] [Indexed: 01/31/2023]
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100
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Pereira V, Mogensen HS, Børsting C, Morling N. Evaluation of the Precision ID Ancestry Panel for crime case work: A SNP typing assay developed for typing of 165 ancestral informative markers. Forensic Sci Int Genet 2017; 28:138-145. [DOI: 10.1016/j.fsigen.2017.02.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 11/24/2022]
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