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Zhang J, Li X, Li L, Chen A, Zhang S. Y-STR analysis of highly degraded DNA from skeletal remains over 70 years old. Forensic Sci Res 2024; 9:owae020. [PMID: 38617445 PMCID: PMC11014468 DOI: 10.1093/fsr/owae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/18/2023] [Indexed: 04/16/2024] Open
Abstract
The goal of the following study is to clarify whether the skeletal remains over 70 years old from missing persons and their alleged relatives shared identical Y-STR loci. Nowadays, advances in ancient DNA extraction techniques and approaches of using multiple different Y-STRs have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Given the ages and conditions of the skeletal remains, ancient DNA extraction methods can be used to maximize the probability of DNA recovery. Considering that information about distant relatives is more relevant for long-term missing persons and alleged family members are male, Y-STR loci analysis is considered the most appropriate and informative approach for determining paternal lineage relationship. In this study, Y-STR genotypes obtained from these alleged relatives were identical to each other and to the alleles of missing persons' consensus profiles at more than 22 loci examined, whilst not being found in Y-STR population database from Y-Chromosome STR Haplotype Reference Database. Therefore, Missing Person No.7 and Missing Person No.18 have a patrilineal relationship with reference samples from Family1 and Family2, respectively. In addition, the fact that Y-STR haplotypes obtained from skeletal remains of missing persons and reference samples are not found in the Han Chinese people from East Asian demonstrates its rarity and further supports a paternal lineage relationship amongst them.
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Affiliation(s)
- Jiashuo Zhang
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun, China
| | - Xuebo Li
- Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan, China
- Institute of Forensic Science, Shandong University of Political Science and Law, Jinan, China
| | - Liangliang Li
- Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan, China
- Institute of Forensic Science, Shandong University of Political Science and Law, Jinan, China
| | - Anqi Chen
- Institute of Forensic Science, Fudan University, Shanghai, China
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Suhua Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
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2
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Luo Y, Zhang J, Ni M, Mei Z, Ye Q, Guo B, Fang L, Feng D, Wang L, Yan J, Wang G. Pilot validation of on-field STR typing and human identity testing by MinION nanopore sequencing. Electrophoresis 2024; 45:885-896. [PMID: 38356010 DOI: 10.1002/elps.202300234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
Nanopore sequencing technology has broad application prospects in forensic medicine due to its small size, portability, fast speed, real-time result analysis capabilities, single-molecule sequencing abilities, and simple operation. Here, we demonstrate for the first time that nanopore sequencing platforms can be used to identify individuals in the field. Through scientific and reasonable design, a nanopore MinION MK1B device and other auxiliary devices are integrated into a portable detection box conducive to individual identification at the accident site. Individual identification of 12 samples could be completed within approximately 24 h by jointly detecting 23 short tandem repeat (STR) loci. Through double-blinded experiments, the genotypes of 49 samples were successfully determined, and the accuracy of the STR genotyping was verified by the gold standard. Specifically, the typing success rate for 1150 genotypes was 95.3%, and the accuracy rate was 86.87%. Although this study focused primarily on demonstrating the feasibility of full-process testing, it can be optimistically predicted that further improvements in bioinformatics workflows and nanopore sequencing technology will help enhance the feasibility of Oxford Nanopore Technologies equipment for real-time individual identification at accident sites.
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Affiliation(s)
- Yuan Luo
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Jiarong Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing, P. R. China
| | - Zhusong Mei
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Qiao Ye
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Bingqian Guo
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Longmei Fang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Dongyun Feng
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Lu Wang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Guangyun Wang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
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Rahmat RA, Humphries MA, Saedon NA, Self PG, Linacre AMT. Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth. Int J Legal Med 2023; 137:1353-1360. [PMID: 37306739 DOI: 10.1007/s00414-023-03017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023]
Abstract
Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat. Poor DNA quality can negatively affect the success of DNA analysis towards human identification. The process of isolating DNA from biological samples is arduous and costly. Thus, an informative pre-screening method that could aid in selecting samples that can potentially yield amplifiable DNA would be of excellent value. A multiple linear regression model to predict the DNA content in incinerated pig teeth was developed based on the colourimetry, HA crystallite size and quantified nuclear and mitochondrial DNA. The chromaticity a* was found to be a significant predictor of the regression model. This study outlines a method to predict the viability of extracting nuclear and mitochondrial DNA from pig teeth that were exposed to a wide range of temperatures (27 to 1000 °C) with high accuracy (99.5-99.7%).
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Affiliation(s)
- Rabiah A Rahmat
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Melissa A Humphries
- School and Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, 5006, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, the University of Adelaide, Adelaide, South Australia, Australia
| | - Nor A Saedon
- Forensic DNA Division, Forensic Science Analysis Centre, Department of Chemistry, Selangor, 46661, Malaysia
| | - Peter G Self
- CSIRO, Land and Water, Locked Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Adrian M T Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, 5042, Australia
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Aguilar-Velázquez JA, Llamas-de-Dios BJ, Córdova-Mercado MF, Coronado-Ávila CE, Salas-Salas O, López-Quintero A, Ramos-González B, Rangel-Villalobos H. Accuracy of Eye and Hair Color Prediction in Mexican Mestizos from Monterrey City Based on ForenSeq TM DNA Signature Prep. Genes (Basel) 2023; 14:genes14051120. [PMID: 37239480 DOI: 10.3390/genes14051120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Forensic genomic systems allow simultaneously analyzing identity informative (iiSNPs), ancestry informative (aiSNPs), and phenotype informative (piSNPs) genetic markers. Among these kits, the ForenSeq DNA Signature prep (Verogen) analyzes identity STRs and SNPs as well as 24 piSNPs from the HIrisPlex system to predict the hair and eye color. We report herein these 24 piSNPs in 88 samples from Monterrey City (Northeast, Mexico) based on the ForenSeq DNA Signature prep. Phenotypes were predicted by genotype results with both Universal Analysis Software (UAS) and the web tool of the Erasmus Medical Center (EMC). We observed predominantly brown eyes (96.5%) and black hair (75%) phenotypes, whereas blue eyes, and blond and red hair were not observed. Both UAS and EMC showed high performance in eye color prediction (p ≥ 96.6%), but a lower accuracy was observed for hair color prediction. Overall, UAS hair color predictions showed better performance and robustness than those obtained with the EMC web tool (when hair shade is excluded). Although we employed a threshold (p > 70%), we suggest using the EMC enhanced approach to avoid the exclusion of a high number of samples. Finally, although our results are helpful to employ these genomic tools to predict eye color, caution is suggested for hair color prediction in Latin American (admixed) populations such as those studied herein, principally when no black color is predicted.
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Affiliation(s)
- José Alonso Aguilar-Velázquez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
- Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Blanca Jeannete Llamas-de-Dios
- Licenciatura en Ciencias Forenses, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Miranda Fabiola Córdova-Mercado
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Carolina Elena Coronado-Ávila
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Orlando Salas-Salas
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Andrés López-Quintero
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Benito Ramos-González
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCI-UdeG), Ocotlán 47820, Jalisco, Mexico
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Zupanič Pajnič I, Leskovar T, Črešnar M. Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology. Int J Legal Med 2023:10.1007/s00414-023-03003-3. [PMID: 37127762 DOI: 10.1007/s00414-023-03003-3] [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: 02/02/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 107 (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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Zupanič Pajnič I, Geršak ŽM, Leskovar T, Črešnar M. Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site. Forensic Sci Int Genet 2023; 65:102886. [PMID: 37137206 DOI: 10.1016/j.fsigen.2023.102886] [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: 12/15/2022] [Revised: 03/31/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Živa Miriam Geršak
- Institute of Radiology, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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7
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Adams B, Warnke-Sommer J, Odien J, Soler A, Damann F. Victim identification from the September 11, 2001 attack on the World Trade Center: Past trends and future projections. Forensic Sci Int 2022; 340:111463. [PMID: 36150280 DOI: 10.1016/j.forsciint.2022.111463] [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: 07/19/2022] [Accepted: 09/08/2022] [Indexed: 11/25/2022]
Abstract
Victim identification following mass fatality events is critically important. Extensive traumatic injuries and body fragmentation add complexity to this process. World Trade Center (WTC) identification efforts have been ongoing for over 20 years and this study tracks identification trends from the 2753 known WTC victims and the 21,905 recovered remains. For identified victims, data include the number of remains identified, date(s) of the identification(s), and identification modalities. Results show a heavy reliance on DNA due to body fragmentation. Other modalities played an important role initially, but DNA eventually became the singular identification modality. For large-scale disasters involving significant body fragmentation, aggressive DNA testing strategies are critical for victim identification. Over time, the number of linked remains (portions of previously identified individuals) will greatly outnumber the new identifications (first-time identifications). A novel approach using statistical modeling from ecology studies was applied to estimate future WTC identification rates using Identification Accumulation Curve extrapolation with the Good-Toulmin estimator. Projections indicate there will be 76 first-time identifications (95% CI: 49-117) through the successful DNA testing of 3404 unidentified, fragmentary remains. The remainder of the identifications would be additional portions of previously identified victims. These results may be instructional for management of other large-scale, protracted victim identification efforts.
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Affiliation(s)
- Bradley Adams
- New York City Office of Chief Medical Examiner, 520 First Avenue, New York, NY 10016, USA.
| | - Julia Warnke-Sommer
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA; Defense POW/MIA Accounting Agency, 106 Peacekeeper Drive, Bldg. 301D, Offutt AFB, NE 68113, USA
| | - Jennifer Odien
- New York City Office of Chief Medical Examiner, 520 First Avenue, New York, NY 10016, USA
| | - Angela Soler
- New York City Office of Chief Medical Examiner, 520 First Avenue, New York, NY 10016, USA
| | - Franklin Damann
- Defense POW/MIA Accounting Agency, 106 Peacekeeper Drive, Bldg. 301D, Offutt AFB, NE 68113, USA
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Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing. PLoS One 2022; 17:e0266332. [PMID: 35363835 PMCID: PMC8974964 DOI: 10.1371/journal.pone.0266332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/19/2022] [Indexed: 11/23/2022] Open
Abstract
Objectives To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT). Methods DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) haplotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. Subsequentlly, the paternity testing parameters were attributed to each case quantitatively. Results The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699–99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation. Conclusions Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.
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Gehrig C, Delémont S, Comte J, Hicks T, Basset P, Grosjean F, Dion D, Cossu C, Bottinelli M, Hecht M, Sulzer A, Voegeli P, Castella V. A Swiss collaborative exercise for Disaster Victim Identification (DVI): Covering situations with different levels of complexity. J Forensic Leg Med 2021; 83:102254. [PMID: 34592483 DOI: 10.1016/j.jflm.2021.102254] [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: 05/26/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 11/27/2022]
Abstract
The identification of victims of a disaster (DVI) requires the collaboration of different specialists. Within a DVI context, DNA analyses often play an important role. Consequently, forensic genetic laboratories should be prepared to cope with DVI situations, as this can involve large-scale DNA profile comparisons. Six forensic genetic laboratories from Switzerland participated in an exercise where supposedly a plane had crashed. The goal of the exercise was to monitor participants use of dedicated software with ground truth cases and to make them aware of the existence of particular situations that may occur in real cases. For assigning the value of the comparison of the DNA profiles, all participating laboratories used the DVI module of Familias v3.2.1 In addition, one of the 6 laboratories used the Pedigree Searcher from CODIS v7.0. The data (AmpFlSTR® NGM SElect™ profiles) were generated to challenge the participating laboratories: cases with first, second degree biological parents, mutation events, as well as non-paternity cases were included. This study shows that the majority of the participants used the software in an appropriate way. However, a few misleading conclusions were detected for the most challenging situations. These errors belonged to one of the following categories: false pedigree, false association using the higher LR, misleading contextual information (false paternity) and not clustering family members. Specific recommendations are provided in order to reduce misuse of the software and the risk of misinterpretations by using all the relevant information.
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Affiliation(s)
- Christian Gehrig
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland.
| | | | - Jennifer Comte
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland
| | - Tacha Hicks
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland; Fondation pour la Formation Continue Universitaire Lausannoise (UNIL-EPFL), Switzerland
| | - Patrick Basset
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland
| | | | - Daniel Dion
- Institut für Rechtsmedizin, Basel, Switzerland
| | | | | | - Mirco Hecht
- Institut für Rechtsmedizin, Bern, Switzerland
| | | | | | - Vincent Castella
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland
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Interpretation of DNA data within the context of UK forensic science - investigation. Emerg Top Life Sci 2021; 5:395-404. [PMID: 34151948 PMCID: PMC8457768 DOI: 10.1042/etls20210165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/08/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022]
Abstract
This article is the second part of a review of the interpretation of DNA data in forensic science. The first part describes the evaluation of autosomal profile for criminal trials where an evidential weight is assigned to the profile of a person of interest (POI) and a crime-scene profile. This part describes the state of the art and future advances in the interpretation of forensic DNA data for providing intelligence information during an investigation. Forensic DNA is crucial in the investigative phase of an undetected crime where a POI needs to be identified. A sample taken from a crime scene is profiled using a range of forensic DNA tests. This review covers investigation using autosomal profiles including searching national and international crime and reference DNA databases. Other investigative methodologies described are kinship analysis; familial searching; Y chromosome (Y-STR) and mitochondrial (mtDNA) profiles; appearance prediction and geographic ancestry; forensic genetic genealogy; and body identification. For completeness, the evaluation of Y-STRs, mtDNA and kinship analysis are briefly described. Taken together, parts I and II, cover the range of interpretation of DNA data in a forensic context.
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11
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Zupanič Pajnič I. Identification of a Slovenian prewar elite couple killed in the Second World War. Forensic Sci Int 2021; 327:110994. [PMID: 34536754 DOI: 10.1016/j.forsciint.2021.110994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Abstract
Genetic identification of a Slovenian prewar elite couple killed in 1944 was performed by typing autosomal and Y-chromosomal STRs, and phenotypic HIrisPlex SNPs for hair and eye color prediction were analyzed for the female skeleton using next-generation sequencing (NGS) technology. The clandestine grave containing the couple's skeletal remains was found in 2015 and only the partial remains were found. Living distant relatives could be found only for the male victim. Because of a lack of comparative reference samples, it was not possible to identify the female victim through autosomal and mitochondrial DNA typing. However, the possibility of comparison of eye and hair color with a painting exhibited in the City Museum of Ljubljana by the prominent Slovenian painter Ivana Kobilca existed. Nuclear DNA obtained from the samples was quantified using the PowerQuant System, and then STR typing was carried out with different autosomal and Y-STR kits. From 0.09-9.36 ng DNA/g of powder was obtained from teeth and bones analyzed. Complete autosomal and Y-STR profiles made it possible to identify the male skeleton via comparison with two nephews. For the female victim, predicted eye and hair color was compared to colors on the painting. Kobilca's painting confirms the genetically predicted eye and hair color. After more than seventy years, the skeletal remains of the couple were handed over to their relatives, who buried the victims with dignity in a family grave.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
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12
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Loockerman C, Miller B, Ramsey R, Hughes S, Houston R. Collection and storage of DVI samples with microFLOQ® Direct swabs for direct amplification. Forensic Sci Int Genet 2021; 55:102588. [PMID: 34488175 DOI: 10.1016/j.fsigen.2021.102588] [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: 04/10/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
The rapid identification of decomposing human remains is a crucial component of disaster victim identification (DVI), often occurring in remote areas without access to laboratory or storage facilities. Due to the ease of collection and amenability to storage in harsh conditions, swabs may be used to collect DNA from decomposing remains as an alternative to sampling tissue or bone. Direct amplification could further streamline the process and reduce costs. This study investigated the efficacy of direct amplification of DVI samples using microFLOQ® Direct swabs and the QIAGEN Investigator QS GO! Kit. A comparison of performance between direct amplification and traditional methods was made to assess whether direct amplification offered an improvement to traditional methods. DNA was collected by swabbing the muscle of a decomposing human cadaver using three swab types (ADS Genetics 4N6FLOQSwabs®, NADS Genetics 4N6FLOQSwabs®, and the microFLOQ® Direct swab). Traditional swabs (4N6FLOQSwabs®) were extracted and quantified, while a direct amplification strategy was used with the microFLOQ® Direct swabs coupled with the Investigator 24Plex GO! Kit. Processing of the microFLOQ® Direct swabs were optimized and a hybrid strategy that used 4N6FLOQSwabs® to collect and store DNA before swabbing or "subsampling" the 4N6FLOQSwabs® for processing with microFLOQ® Direct swabs was developed. This hybrid strategy allowed for rapid processing without the consumption of the original sample. Traditional and direct PCR methods were comparable up to day 10 of decomposition depending on the sample location and for up to 3 months of storage at room temperature. This research indicated that microFLOQ® Direct swabs in conjunction with the Investigator 24Plex GO! Kit can be used to facilitate rapid direct processing of DNA from decomposing human remains.
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Affiliation(s)
- Coral Loockerman
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Brittanie Miller
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Rebecca Ramsey
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Sheree Hughes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States.
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13
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Weisz NA, Roberts KA, Hardy WR. Reliability of phenotype estimation and extended classification of ancestry using decedent samples. Int J Legal Med 2021; 135:2221-2233. [PMID: 34436656 DOI: 10.1007/s00414-021-02631-x] [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: 12/16/2020] [Accepted: 06/04/2021] [Indexed: 11/30/2022]
Abstract
The Illumina® MiSeq FGx™, in conjunction with the ForenSeq™ DNA Signature Prep kit, produces genotypes of the CODIS-required short tandem repeats and provides phenotype and biogeographical ancestry estimations via phenotype-informative and ancestry-informative markers, respectively. Although both markers have been validated for use in forensic biology, there is little data to determine the practical utility of these estimations to assist in identifying missing persons using decedent casework samples. The accuracy and utility of phenotypic and ancestral estimations were investigated for 300 samples received by the Los Angeles County Department of Medical Examiner-Coroner. piSNP genotypes were translated into hair and eye colors using the Forenseq™ Universal Analysis Software (UAS) on the MiSeq FGx™ and the HIrisPlex System, and statistical accuracy was evaluated in context with the reported decedent characteristics. Similarly, estimates of each decedent's biogeographical ancestry were compared to assess the efficacy of these markers to predict ancestry correctly. The average UAS and the HIrisPlex system prediction accuracy for brown and blue eyes were 95.3% and 96.2%, respectively. Intermediate eye color could not be predicted with high accuracy using either system. Other than the black hair phenotype reporting an accuracy that exceeded 90% using either system, hair color was also too variable to be predicted with high accuracy. The FROG-kb database distinguishes decedents adequately beyond the Asian, African, European, and Admixed American global ancestries provided by the MiSeq FGx™ UAS PCA plots. FROG-kb correctly identified Middle Eastern, Pacific Islander, Latin American, or Jewish ancestries with accuracies of 70.0%, 81.8%, 73.8%, and 86.7%, respectively.
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Affiliation(s)
- Naomi A Weisz
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA
| | - Katherine A Roberts
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA. .,California Forensic Science Institute, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA.
| | - W Reef Hardy
- Human Genomics Unit, Los Angeles County Department of Medical Examiner-Coroner, 1104 N Mission Road, Los Angeles, CA, 90033, USA
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14
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Manzella AM, Carte KM, King SL, Moreno LI. Assessment of the ANDE 6C Rapid DNA system and investigative biochip for the processing of calcified and muscle tissue. Forensic Sci Int Genet 2021; 53:102526. [PMID: 33991866 DOI: 10.1016/j.fsigen.2021.102526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022]
Abstract
The ANDE 6C Rapid DNA system could offer a potential alternative for the processing of calcified and soft tissue samples, often encountered in mass disaster scenarios. While originally designed for single source buccal swabs, interest in the performance of these instruments when using other types of single source samples continues to grow. To enhance the recovery of otherwise lesser quality samples, the manufacturer developed the investigative biochip, an alternative to the NDIS approved Arrestee biochip for reference sample buccal swabs. This study explores the viability of using the ANDE 6C system and the investigative biochip to process soft and calcified tissue, and uses conventional sample processing to contrast the results. Though the success rate obtained using the instrument's expert system was lower than expected - 0% muscle, 11% ribs, and 50% teeth -, the ANDE 6C offers an advantage over conventional calcified tissue processing in terms of turn-around time and processing complexity. If robust analysis parameters can be established to allow the evaluation of the generated data by a qualified analyst on a third party software platform, the use of the ANDE 6C and investigative biochip could be a suitable alternative for currently employed procedures. However, as is the case with conventional DNA typing, the quantity, age, type of biological material and quality of the exemplars could all play a role in the success of the ANDE 6C typing process. In addition, it appears as if the calcified tissue pre-processing protocol that provides the better opportunity for the ANDE 6C success is not appropriate to be carried out in the field or by non-trained personnel as special equipment as well as a certain level of exe expertise and technique is necessary. Nevertheless, disaster victim and unidentified human remain samples could be processed in a laboratory setting using the Rapid DNA ANDE 6C platform provided sufficient material is available to conduct a second, 'rescue' sample processing if necessary.
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Affiliation(s)
- April M Manzella
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA; EnProVera, 410 Ware Blvd, Tampa, FL 33619, USA
| | - Kathryn M Carte
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA; EnProVera, 410 Ware Blvd, Tampa, FL 33619, USA
| | - Sheria L King
- Scientific Support Services, Royal Bahamas Police Force, East St, Nassau, Bahamas
| | - Lilliana I Moreno
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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15
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Ueland M, Harris S, Forbes SL. Detecting volatile organic compounds to locate human remains in a simulated collapsed building. Forensic Sci Int 2021; 323:110781. [PMID: 33878551 DOI: 10.1016/j.forsciint.2021.110781] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/05/2021] [Accepted: 04/05/2021] [Indexed: 11/21/2022]
Abstract
The occurrence of mass disasters has increased worldwide due to changing environments from global warming and a heightened threat of terrorism acts. When these disasters strike, it is imperative to rapidly locate and recover human victims, both the living and deceased. While search and rescue dogs are used to locate the living, cadaver detection dogs are typically tasked with locating the dead. This can prove challenging because commingling of victims is likely to occur during disasters in populated areas which will impact the decomposition process and the resulting odour produced. To date, there has been no research to investigate the process of human decomposition in a mass disaster scenario or to understand which compounds are detectable by cadaver detection dogs. Hence, the current study investigated the human decomposition process and subsequent volatile organic compound (VOC) production in two simulated building collapse scenarios with six human donors placed in each scenario. The human remains were only recovered after a period of one month, during which time VOC samples were collected and analysed using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry. A considerable degree of differential decomposition was observed upon recovery of the human remains, which was carried out as a part of a police disaster victim recovery training exercise. The location of the bodies in the disaster area was found to impact the decomposition process. The VOC profile was found to correlate with the decomposition process. Fifteen days following the simulated disaster, the VOC profile changed showing that a detectable change in the decomposition process had occurred. Overall, the changing VOC profile can inform the training of cadaver detection dogs for these unique scenarios.
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Affiliation(s)
- Maiken Ueland
- Centre for Forensic Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia.
| | - Scott Harris
- CBR/DVI Unit, Crime Scene Group, Forensic Services Department, Victoria Police, Forensic Services Centre, 31 Forensic Drive, Macleod, VIC 3085, Australia
| | - Shari L Forbes
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, G8Z 4M3 Québec, Canada
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16
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Mckinnon M, Henneberg M, Higgins D. A review of the current understanding of burned bone as a source of DNA for human identification. Sci Justice 2021; 61:332-338. [PMID: 34172121 DOI: 10.1016/j.scijus.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/16/2021] [Accepted: 03/13/2021] [Indexed: 10/21/2022]
Abstract
Identification of incinerated human remains may rely on genetic analysis of burned bone which can prove far more challenging than fresh tissues. Severe thermal insult results in the destruction or denaturation of DNA in soft tissues, however genetic material may be preserved in the skeletal tissues. Considerations for DNA retrieval from these samples include low levels of exogenous DNA, the dense, mineralised nature of bone, and the presence of contamination, and qPCR inhibitors. This review collates current knowledge in three areas relating to optimising DNA recovery from burned bone: 1) impact of burning on bone and subsequent effects on sample collection, 2) difficulties of preparing burned samples for DNA extraction, and 3) protocols for bone decalcification and DNA extraction. Bone decalcification and various DNA extraction protocols have been tested and optimised for ancient bone, suggesting that prolonged EDTA (Ethylenediaminetetraacetic acid) demineralisation followed by solid-phased silica-based extraction techniques provide the greatest DNA yield. However, there is significantly less literature exploring the optimal protocol for incinerated bones. Although burned bone, like ancient and diagenetic bone, can be considered "low-copy", the taphonomic processes occurring are likely different. As techniques developed for ancient samples are tailored to deal with bone that has been altered in a particular way, it is important to understand if burned bone undergoes similar or different changes. Currently the effects of burning on bone and the DNA within it is not fully understood. Future research should focus on increasing our understanding of the effects of heat on bone and on comparing the outcome of various DNA extraction protocols for these tissues.
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Affiliation(s)
- Meghan Mckinnon
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia.
| | - Maciej Henneberg
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia
| | - Denice Higgins
- Forensic Odontology Unit, Adelaide Dental School, the University of Adelaide, Adelaide, Australia
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17
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Gin K, Tovar J, Bartelink EJ, Kendell A, Milligan C, Willey P, Wood J, Tan E, Turingan RS, Selden RF. The 2018 California Wildfires: Integration of Rapid DNA to Dramatically Accelerate Victim Identification. J Forensic Sci 2020; 65:791-799. [PMID: 32128817 PMCID: PMC7318200 DOI: 10.1111/1556-4029.14284] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/28/2019] [Accepted: 01/03/2020] [Indexed: 12/02/2022]
Abstract
In November 2018, Butte County, California, was decimated by the Camp Fire, the deadliest wildfire in state history. Over 150,000 acres were destroyed, and at its peak, the fire consumed eighty acres per minute. The speed and intensity of the oncoming flames killed scores of people, and weeks before the fire was contained, first responders began searching through the rubble of 18,804 residences and commercial buildings. As with most mass disasters, conventional identification modalities (e.g., fingerprints, odontology, hardware) were utilized to identify victims. The intensity and duration of the fire severely degraded most of the remains, and these approaches were useful in only 22 of 84 cases. In the past, the remaining cases would have been subjected to conventional DNA analysis, which may have required months to years. Instead, Rapid DNA technology was utilized (in a rented recreational vehicle outside the Sacramento morgue) in the victim identification effort. Sixty‐nine sets of remains were subjected to Rapid DNA Identification and, of these, 62 (89.9%) generated short tandem repeat profiles that were subjected to familial searching; essentially all these profiles were produced within hours of sample receipt. Samples successfully utilized for DNA identification included blood, bone, liver, muscle, soft tissue of unknown origin, and brain. In tandem with processing of 255 family reference samples, 58 victims were identified. This work represents the first use of Rapid DNA Identification in a mass casualty event, and the results support the use of Rapid DNA as an integrated tool with conventional disaster victim identification modalities.
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Affiliation(s)
- Kim Gin
- Sacramento County Coroner's Office, 4800 Broadway, Sacramento, CA, 95820
| | - Jason Tovar
- Sacramento County Coroner's Office, 4800 Broadway, Sacramento, CA, 95820
| | - Eric J Bartelink
- Department of Anthropology, California State University, 400 West First Street, Chico, CA, 95929
| | - Ashley Kendell
- Department of Anthropology, California State University, 400 West First Street, Chico, CA, 95929
| | - Colleen Milligan
- Department of Anthropology, California State University, 400 West First Street, Chico, CA, 95929
| | - P Willey
- Department of Anthropology, California State University, 400 West First Street, Chico, CA, 95929
| | - James Wood
- Sonoma County Sheriff-Coroner Office, 3336 Chanate Road, Santa Rosa, CA, 95404
| | - Eugene Tan
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 024551
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18
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Bertoglio B, Grignani P, Di Simone P, Polizzi N, De Angelis D, Cattaneo C, Iadicicco A, Fattorini P, Presciuttini S, Previderè C. Disaster victim identification by kinship analysis: the Lampedusa October 3rd, 2013 shipwreck. Forensic Sci Int Genet 2020; 44:102156. [DOI: 10.1016/j.fsigen.2019.102156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 12/30/2022]
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19
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Zupanič Pajnič I, Obal M, Zupanc T. Identifying victims of the largest Second World War family massacre in Slovenia. Forensic Sci Int 2020; 306:110056. [DOI: 10.1016/j.forsciint.2019.110056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/25/2023]
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20
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Next generation sequencing technology in Second World War victim identification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Almohammed E, Dragana Z, Hadi S. A study of skeletal remains using GlobalFiler™. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Turingan RS, Brown J, Kaplun L, Smith J, Watson J, Boyd DA, Steadman DW, Selden RF. Identification of human remains using Rapid DNA analysis. Int J Legal Med 2019; 134:863-872. [PMID: 31781850 PMCID: PMC7181457 DOI: 10.1007/s00414-019-02186-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/15/2019] [Indexed: 11/16/2022]
Abstract
Rapid identification of human remains following mass casualty events is essential to bring closure to family members and friends of the victims. Unfortunately, disaster victim identification, missing persons identification, and forensic casework analysis are often complicated by sample degradation due to exposure to harsh environmental conditions. Following a mass disaster, forensic laboratories may be overwhelmed by the number of dissociated portions that require identification and reassociation or compromised by the event itself. The interval between the disaster and receipt of victim samples at a laboratory is critical in that sample quality deteriorates as the postmortem interval increases. When bodies decompose due to delay in collection, transport, and sample processing, DNA becomes progressively fragmented, adversely impacting identification. We have previously developed a fully automated, field-forward Rapid DNA identification system that produces STR profiles (also referred to as DNA IDs or DNA fingerprints) from buccal and crime scene samples. The system performs all sample processing and data interpretation in less than 2 h. Here, we present results on Rapid DNA identification performed on several tissue types (including buccal, muscle, liver, brain, tooth, and bone) from exposed human bodies placed above ground or stored in a morgue/cooler, two scenarios commonly encountered following mass disasters. We demonstrate that for exposed remains, buccal swabs are the sample of choice for up to 11 days exposure and bone and tooth samples generated excellent DNA IDs for the 1-year duration of the study. For refrigerated remains, all sample types generated excellent DNA IDs for the 3-month testing period.
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Affiliation(s)
| | - Jessi Brown
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 02451, USA
| | - Ludmila Kaplun
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 02451, USA
| | - Jake Smith
- Department of Anthropology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA
| | - Jenna Watson
- Department of Anthropology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA
| | - Derek A Boyd
- Department of Anthropology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA
| | - Dawnie Wolfe Steadman
- Department of Anthropology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA
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23
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Khatoon F. RECENT TECHNIQUES BASED ON THE UTILIZATION OF DNA AND AUTOSOMAL SINGLE NUCLEOTIDE POLYMORPHISMS FOR IDENTIFYING HUMANS. GOMAL JOURNAL OF MEDICAL SCIENCES 2019. [DOI: 10.46903/gjms/17.02.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The biological samples used in forensics can contain DNA which is highly fragmented as a consequence of exposure to any of the numerous degrading factors. Analysis of the sequence or size of the products of Polymerase chain reaction is at present responsible for the analysis of remains of humans in forensics. Despite the effectiveness of protocols based on PCR, there are certain limitations that are presented by the low numbers of copies of the template and the variations that are imposed by the decaying process to the template. The primary aim of this research is to explore the significance of autosomal SNPs in forensic science through the identification of humans at a crime scene. This study provides an exploration of the applicability of autosomal SNPs for the identification of humans at crime scene. This would fill the gap present in the current literature regarding the significance of autosomal SNPs in the identification of humans during crime scene investigation. It will also enable the identification of the criminals involved in several types of the crimes ranging from general theft to rape and sexual assault, murder, and robberies. It will also allow the identification of dead bodies in cases where it is difficult to identify the dead person due to unrecognizable condition of the body. This study will facilitate the improvement of the investigation of crime scene investigators. It will provide a significant way for the incorporation of recent techniques of the molecular genetics into forensics. Reduction in the workload of the crime scene investigators would also occur through the implementation of outcomes of this study into the field of forensic science. There are several studies which have demonstrated the applicability of SNPs in forensic investigations for identifying the humans at crime scene. Several effective and efficient technological systems have been developed by the researchers which are capable of performing analysis of biological samples containing degraded DNA because SNPs can be obtained from these samples. Physical characteristics of the individuals can be predicted through the analysis of SNPs. This can provide significant information about the color of eye, hair and skin of the individuals involved in crime.
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van Oorschot RA, Szkuta B, Meakin GE, Kokshoorn B, Goray M. DNA transfer in forensic science: A review. Forensic Sci Int Genet 2019; 38:140-166. [DOI: 10.1016/j.fsigen.2018.10.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
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Issan Y, Avlas O, Daniel O. Investigation of Different Ways in Which the
CODIS
7.0 May be Used in Mass Disaster Identification. J Forensic Sci 2018; 64:852-856. [DOI: 10.1111/1556-4029.13915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Yossi Issan
- DNA Database Laboratory Division of Identification and Forensic Science (DIFS) Israel Police Jerusalem Israel
| | - Orna Avlas
- DNA Database Laboratory Division of Identification and Forensic Science (DIFS) Israel Police Jerusalem Israel
| | - Orit Daniel
- DNA Database Laboratory Division of Identification and Forensic Science (DIFS) Israel Police Jerusalem Israel
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26
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de Boer HH, Maat GJ, Kadarmo DA, Widodo PT, Kloosterman AD, Kal AJ. DNA identification of human remains in Disaster Victim Identification (DVI): An efficient sampling method for muscle, bone, bone marrow and teeth. Forensic Sci Int 2018; 289:253-259. [DOI: 10.1016/j.forsciint.2018.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/27/2018] [Indexed: 10/14/2022]
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27
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Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains. Int J Legal Med 2018; 132:1545-1553. [DOI: 10.1007/s00414-018-1794-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
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Challenges in the identification of dead migrants in the Mediterranean: The case study of the Lampedusa shipwreck of October 3rd 2013. Forensic Sci Int 2018; 285:121-128. [PMID: 29482110 DOI: 10.1016/j.forsciint.2018.01.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/31/2018] [Accepted: 01/31/2018] [Indexed: 11/23/2022]
Abstract
Every year thousands of migrants die during the endeavour to reach the Italian coasts, making the Mediterranean the theatre of one of the greatest tragedies of mankind. Over 60% of these victims is buried unidentified: one of the reasons behind this is related to the specific difficulties and lack of strategies concerning AM and PM data collection. The present article describes how Italy is trying to face the problem of migrant identification, thanks to the collaboration between government, the Italian national police and universities. In particular, this is the first pilot study carried out to identify the victims of the second greatest tragedy of its kind off the Italian coast, near Lampedusa, on October 3rd 2013, which caused 366 victims. The present article shows the strategies conceived to collect postmortem and especially antemortem data and to compare them to identify matches, using medicolegal, anthropological, odontological and genetic approaches. Thirty-one victims out of 53 missing sought by relatives were identified (58.5%). The type and the quality of antemortem data available, generally photos and videos, pinpoints the importance of the face and the body for identification when the bodies are well preserved and how DNA analyses may at times present difficulties. In fact, critical points emerged concerning especially the lack of genetic information of the populations to which the victims belonged, the number of genetic markers needed to reach a statistical support for the identification and the need to adopt lineage markers such as mitochondrial DNA and Y-chromosome polymorphisms to identify parental relationships. This pilot study however has proven that families continue to seek their relatives and that it is possible, as well as mandatory, to identify migrant victims in spite of the difficulties in the collection of antemortem and postmortem data. In addition, considering the peculiar scenario, novel strategies for positive identification have to be defined in each field (anthropological, odontological and genetic) as well as in combination.
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29
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Alfonse LE, Garrett AD, Lun DS, Duffy KR, Grgicak CM. A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt. Forensic Sci Int Genet 2018; 32:62-70. [DOI: 10.1016/j.fsigen.2017.10.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/07/2017] [Accepted: 10/20/2017] [Indexed: 01/15/2023]
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30
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Consent process for US-based family reference DNA samples. Forensic Sci Int Genet 2018; 32:71-79. [DOI: 10.1016/j.fsigen.2017.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/12/2017] [Accepted: 10/28/2017] [Indexed: 11/23/2022]
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31
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Kling D, Egeland T, Piñero MH, Vigeland MD. Evaluating the statistical power of DNA-based identification, exemplified by ‘The missing grandchildren of Argentina’. Forensic Sci Int Genet 2017; 31:57-66. [DOI: 10.1016/j.fsigen.2017.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 11/16/2022]
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The use of forensic DNA analysis in humanitarian forensic action: The development of a set of international standards. Forensic Sci Int 2017; 278:221-227. [DOI: 10.1016/j.forsciint.2017.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 05/29/2017] [Accepted: 07/02/2017] [Indexed: 02/05/2023]
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Chaitanya L, Pajnič IZ, Walsh S, Balažic J, Zupanc T, Kayser M. Bringing colour back after 70 years: Predicting eye and hair colour from skeletal remains of World War II victims using the HIrisPlex system. Forensic Sci Int Genet 2016; 26:48-57. [PMID: 27780108 DOI: 10.1016/j.fsigen.2016.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 09/26/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
Abstract
Retrieving information about externally visible characteristics from DNA can provide investigative leads to find unknown perpetrators, and can also help in disaster victim and other missing person identification cases. Aiming for the application to both types of forensic casework, we previously developed and forensically validated the HIrisPlex test system enabling parallel DNA prediction of eye and hair colour. Although a recent proof-of-principle study demonstrated the general suitability of the HIrisPlex system for successfully analysing DNA from bones and teeth of various storage times and conditions, practical case applications to human remains are scarce. In this study, we applied the HIrisPlex system to 49 DNA samples obtained from bones or teeth of World War II victims excavated at six sites, mostly mass graves, in Slovenia. PCR-based DNA quantification ranged from 4pg/μl to 313pg/μl and on an average was 41pg/μl across all samples. All 49 samples generated complete HIrisPlex profiles with the exception of one MC1R DNA marker (N29insA) missing in 83.7% of the samples. In 44 of the 49 samples (89.8%) complete 15-loci autosomal STR (plus amelogenin) profiles were obtained. Of 5 pairs of skeletal remains for which STR profiling suggested an origin in the same individuals, respectively, 4 showed the same HIrisPlex profiles and predicted eye and hair colours, respectively, while discrepancies in one pair (sample 26 and 43) are likely to be explained by DNA quantity and quality issues observed in sample 43. Sample 43 had the lowest DNA concentration of only 4pg/μl, producing least reliable STR results and could be misleading in concluding that samples 43 and 26 originate from the same individual. The HIrisPlex-predicted eye and hair colours from two skeletal samples, suggested to derive from two brothers via STR profiling together with a living sister, were confirmed by the living sister's report. Overall, we demonstrate that after more than 70 years, HIrisPlex-based eye and hair colour prediction from skeletal remains is feasible with high success rate. Our results further encourage the use of the HIrisPlex system in missing person/disaster victim identification to aid the identification process in cases where ante-mortem samples or putative relatives are not directly available, and DNA predicted eye and hair colour information provides leads for locating them, allowing STRbased individual identification.
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Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jože Balažic
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Does zero really mean nothing?-first experiences with the new PowerQuant(TM) system in comparison to established real-time quantification kits. Int J Legal Med 2016; 130:935-940. [PMID: 26972802 DOI: 10.1007/s00414-016-1352-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/25/2016] [Indexed: 10/22/2022]
Abstract
DNA quantification is an important step in the molecular genetic analysis of a forensic sample, hopefully providing reliable data on DNA content for a subsequent generation of reproducible STR profiles for identification. For several years, this quantification has usually been done by real-time PCR protocols and meanwhile a variety of assays are commercially available from different companies. The newest one is the PowerQuant(TM) assay by Promega Inc. which is advertised with the promise that a determined DNA concentration of 0 ng/μl in a forensic sample guarantees the impossibility to achieve true STR results, thus allowing to exclude such samples from STR analysis to save time and money. Thus, the goal of this study was to thoroughly verify the quantification step with regard to its suitability as a screening method. We have evaluated the precision and reliability of four different real-time PCR quantification assays by systematically testing DNA dilutions and forensic samples with various DNA contents. Subsequently, each sample was subjected to the Powerplex® ESX 17 fast kit to determine a reliable cutoff level for exclusion of definitely negative samples from STR analysis. An accurate quantification of different cell line DNA dilutions was not possible with any kit. However, at least the PowerQuant(TM) assay provided suitable data analyzing forensic samples, whereas in other systems up to 46 % of negative samples still displayed reliable STR analysis results. All in all, the PowerQuant(TM) assay represents a big step forward, but the evaluation of real-time PCR quantification results has still to be done with great care.
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Vullo CM, Romero M, Catelli L, Šakić M, Saragoni VG, Jimenez Pleguezuelos MJ, Romanini C, Anjos Porto MJ, Puente Prieto J, Bofarull Castro A, Hernandez A, Farfán MJ, Prieto V, Alvarez D, Penacino G, Zabalza S, Hernández Bolaños A, Miguel Manterola I, Prieto L, Parsons T. GHEP-ISFG collaborative simulated exercise for DVI/MPI: Lessons learned about large-scale profile database comparisons. Forensic Sci Int Genet 2015; 21:45-53. [PMID: 26716885 DOI: 10.1016/j.fsigen.2015.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 11/24/2022]
Abstract
The GHEP-ISFG Working Group has recognized the importance of assisting DNA laboratories to gain expertise in handling DVI or missing persons identification (MPI) projects which involve the need for large-scale genetic profile comparisons. Eleven laboratories participated in a DNA matching exercise to identify victims from a hypothetical conflict with 193 missing persons. The post mortem database was comprised of 87 skeletal remain profiles from a secondary mass grave displaying a minimal number of 58 individuals with evidence of commingling. The reference database was represented by 286 family reference profiles with diverse pedigrees. The goal of the exercise was to correctly discover re-associations and family matches. The results of direct matching for commingled remains re-associations were correct and fully concordant among all laboratories. However, the kinship analysis for missing persons identifications showed variable results among the participants. There was a group of laboratories with correct, concordant results but nearly half of the others showed discrepant results exhibiting likelihood ratio differences of several degrees of magnitude in some cases. Three main errors were detected: (a) some laboratories did not use the complete reference family genetic data to report the match with the remains, (b) the identity and/or non-identity hypotheses were sometimes wrongly expressed in the likelihood ratio calculations, and (c) many laboratories did not properly evaluate the prior odds for the event. The results suggest that large-scale profile comparisons for DVI or MPI is a challenge for forensic genetics laboratories and the statistical treatment of DNA matching and the Bayesian framework should be better standardized among laboratories.
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Affiliation(s)
- Carlos M Vullo
- Equipo Argentino de Antropología Forense (EAAF), Córdoba, Argentina.
| | - Magdalena Romero
- Equipo Argentino de Antropología Forense (EAAF), Córdoba, Argentina
| | - Laura Catelli
- Equipo Argentino de Antropología Forense (EAAF), Córdoba, Argentina
| | - Mustafa Šakić
- International Commission for Missing Persons (ICMP), USA
| | | | - María Jose Jimenez Pleguezuelos
- Unitat Central de Laboratori Biològic, Divisió de Policia Científica, Policia de la Generalitat-Mossos d'Esquadra, BCN, Spain
| | - Carola Romanini
- Equipo Argentino de Antropología Forense (EAAF), Córdoba, Argentina
| | | | | | | | - Alexis Hernandez
- Instituto Nacional de Toxicología y Ciencias Forenses, (INTCF), Canarias, Spain
| | - María José Farfán
- Instituto Nacional de Toxicología y Ciencias Forenses, (INTCF), Madrid, Spain
| | - Victoria Prieto
- Instituto Nacional de Toxicología y Ciencias Forenses, (INTCF), Sevilla, Spain
| | - David Alvarez
- Laboratorio de ADN, Unidad Central de Análisis Científicos, Comisaría General de Policía Científica, Madrid, Spain
| | | | | | | | | | - Lourdes Prieto
- Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Spain
| | - Thomas Parsons
- International Commission for Missing Persons (ICMP), USA
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Ossowski A, Kuś M, Kupiec T, Bykowska M, Zielińska G, Jasiński ME, March AL. The Polish Genetic Database of Victims of Totalitarianisms. Forensic Sci Int 2015; 258:41-9. [PMID: 26646737 DOI: 10.1016/j.forsciint.2015.10.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 10/15/2015] [Accepted: 10/29/2015] [Indexed: 11/26/2022]
Abstract
This paper describes the creation of the Polish Genetic Database of Victims of Totalitarianism and the first research conducted under this project. On September 28th 2012, the Pomeranian Medical University in Szczecin and the Institute of National Remembrance-Commission for Prosecution of Crimes against the Polish Nation agreed to support the creation of the Polish Genetic Database of Victims of Totalitarianism (PBGOT, www.pbgot.pl). The purpose was to employ state-of-the-art methods of forensic genetics to identify the remains of unidentified victims of Communist and Nazi totalitarian regimes. The database was designed to serve as a central repository of genetic information of the victim's DNA and that of the victim's nearest living relatives, with the goal of making a positive identification of the victim. Along the way, PGBOT encountered several challenges. First, extracting useable DNA samples from the remains of individuals who had been buried for over half a century required forensic geneticists to create special procedures and protocols. Second, obtaining genetic reference material and historical information from the victim's closest relatives was both problematic and urgent. The victim's nearest living relatives were part of a dying generation, and the opportunity to obtain the best genetic and historical information about the victims would soon die with them. For this undertaking, PGBOT assembled a team of historians, archaeologists, forensic anthropologists, and forensic geneticists from several European research institutions. The field work was divided into five broad categories: (1) exhumation of victim remains and storing their biological material for later genetic testing; (2) researching archives and historical data for a more complete profile of those killed or missing and the families that lost them; (3) locating the victim's nearest relatives to obtain genetic reference samples (swabs), (4) entering the genetic data from both victims and family members into a common database; (5) making a conclusive, final identification of the victim. PGBOT's first project was to identify victims of the Communist regime buried in hidden mass graves in the Powązki Military Cemetery in Warsaw. Throughout 2012 and 2013, PGBOT carried out archaeological exhumations in the Powązki Military Cemetery that resulted in the recovery of the skeletal remains of 194 victims in several mass graves. Of the 194 sets of remains, more than 50 victims have been successfully matched and identified through genetic evidence.
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Affiliation(s)
- A Ossowski
- Department of Forensic Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - M Kuś
- Department of Forensic Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland.
| | - T Kupiec
- Institute of Forensic Research in Krakow, Krakow, Poland
| | - M Bykowska
- Tadeusz Manteuffel Institute of History of the Polish Academy of Sciences, Warsaw, Poland
| | - G Zielińska
- Department of Forensic Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - M E Jasiński
- Department of Historical Studies, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - A L March
- Texas Rio Grande Legal Aid, San Antonio, TX, United States
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A new disaster victim identification management strategy targeting “near identification-threshold” cases: Experiences from the Boxing Day tsunami. Forensic Sci Int 2015; 250:91-7. [DOI: 10.1016/j.forsciint.2015.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/23/2015] [Accepted: 03/10/2015] [Indexed: 11/18/2022]
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The auditory ossicles as a DNA source for genetic identification of highly putrefied cadavers. Int J Legal Med 2015; 129:457-62. [PMID: 25794688 DOI: 10.1007/s00414-015-1177-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
Abstract
Genetic identification of putrefied bodies is a common task in forensic medicine. With advancing putrefaction, however, DNA integrity is rapidly decreasing and genetic typing of tissue might be impaired or impossible. Since DNA stability is generally higher in hard tissues, bones or teeth are frequently used as DNA source in such cases. However, isolation of DNA from hard tissues is usually very time-consuming and labor-intensive. This can be especially important in (forensic) cases where time is short and identification has to be carried out as fast as possible. Here, we present the identification of dead bodies by analyzing DNA from the auditory ossicles. These minuscule bones provided DNA of sufficient quality and quantity for identification purposes in all 40 investigated cases. Additionally, processing of the bones proved to be amazingly easy and fast, and a successful extraction is possible using a variety of different methods. We present a detailed protocol, results, and cases in which this new method has been successfully applied.
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Kling D, Tillmar AO, Egeland T. Familias 3 - Extensions and new functionality. Forensic Sci Int Genet 2014; 13:121-7. [PMID: 25113576 DOI: 10.1016/j.fsigen.2014.07.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 11/16/2022]
Abstract
In relationship testing the aim is to determine the most probable pedigree structure given genetic marker data for a set of persons. Disaster Victim Identification (DVI) based on DNA data from presumed relatives of the missing persons can be considered to be a collection of relationship problems. Forensic calculations in investigative mode address questions like "How many markers and reference persons are needed?" Such questions can be answered by simulations. Mutations, deviations from Hardy-Weinberg Equilibrium (or more generally, accounting for population substructure) and silent alleles cannot be ignored when evaluating forensic evidence in case work. With the advent of new markers, so called microvariants have become more common. Previous mutation models are no longer appropriate and a new model is proposed. This paper describes methods designed to deal with DVI problems and a new simulation model to study distribution of likelihoods. There are softwares available, addressing similar problems. However, for some problems including DVI, we are not aware of freely available validated software. The Familias software has long been widely used by forensic laboratories worldwide to compute likelihoods in relationship scenarios, though previous versions have lacked desired functionality, such as the above mentioned. The extensions as well as some other novel features have been implemented in the new version, freely available at www.familias.no. The implementation and validation are briefly mentioned leaving complete details to Supplementary sections.
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Affiliation(s)
- Daniel Kling
- Department of Family Genetics, Norwegian Institute of Public Health, Oslo, Norway; Department for Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway.
| | - Andreas O Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden.
| | - Thore Egeland
- Department for Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway; Department of Forensic Genetics, Norwegian Institute of Public Health, Oslo, Norway.
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40
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Canturk KM, Emre R, Kınoglu K, Başpınar B, Sahin F, Ozen M. Current status of the use of single-nucleotide polymorphisms in forensic practices. Genet Test Mol Biomarkers 2014; 18:455-60. [PMID: 24754266 DOI: 10.1089/gtmb.2013.0466] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Forensic geneticists often use short tandem repeats (STRs) to solve cases. However, STRs can be insufficient when DNA samples are degraded due to environmental exposure and mass disasters, alleged and real relatives are genetically related in paternity or kinship analyses, or a suspect is lacking. In such cases, single-nucleotide polymorphisms (SNPs) can provide valuable information and thus should be seriously considered as a tool to help resolve challenging cases. In this review, the current status of SNP analyses in forensic applications and the comparative advantages and disadvantages of SNPs with other biomarkers are discussed.
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41
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Appels R, Nystrom-Persson J, Keeble-Gagnere G. Advances in genome studies in plants and animals. Funct Integr Genomics 2014; 14:1-9. [PMID: 24626952 PMCID: PMC3968518 DOI: 10.1007/s10142-014-0364-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 01/30/2023]
Abstract
The area of plant and animal genomics covers the entire suite of issues in biology because it aims to determine the structure and function of genetic material. Although specific issues define research advances at an organism level, it is evident that many of the fundamental features of genome structure and the translation of encoded information to function share common ground. The Plant and Animal Genome (PAG) conference held in San Diego (California), in January each year provides an overview across all organisms at the genome level, and often it is evident that investments in the human area provide leadership, applications, and discoveries for researchers studying other organisms. This mini-review utilizes the plenary lectures as a basis for summarizing the trends in the genome-level studies of organisms, and the lectures include presentations by Ewan Birney (EBI, UK), Eric Green (NIH, USA), John Butler (NIST, USA), Elaine Mardis (Washington, USA), Caroline Dean (John Innes Centre, UK), Trudy Mackay (NC State University, USA), Sue Wessler (UC Riverside, USA), and Patrick Wincker (Genoscope, France). The work reviewed is based on published papers. Where unpublished information is cited, permission to include the information in this manuscript was obtained from the presenters.
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Affiliation(s)
- R Appels
- Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia,
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Ossowski A, Kuś M, Brzeziński P, Prüffer J, Piątek J, Zielińska G, Bykowska M, Jałowińska K, Torgaszev A, Skoryukov A, Parafiniuk M. Example of human individual identification from World War II gravesite. Forensic Sci Int 2013; 233:179-92. [PMID: 24314519 DOI: 10.1016/j.forsciint.2013.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 08/26/2013] [Accepted: 09/02/2013] [Indexed: 11/30/2022]
Abstract
This paper presents the procedure elaborated by our team which was applied to the mode of identification of Red Army soldiers who were taken as prisoners by the German Army during World War II and deceased in captivity. In the course of our search the unmarked burial of ten Soviet prisoners of war was found. Historical, anthropological and genetic research conducted by us led to the personal identification of nine of them, including two by means of DNA analysis.
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Affiliation(s)
- Andrzej Ossowski
- Pomeranian Medical University in Szczecin, Department of Forensic Medicine, Poland; Association "Pomorze1945", Poland; Institute of National Remembrance, Branch Office in Szczecin, Poland
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Roewer L. DNA fingerprinting in forensics: past, present, future. INVESTIGATIVE GENETICS 2013; 4:22. [PMID: 24245688 PMCID: PMC3831584 DOI: 10.1186/2041-2223-4-22] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 11/29/2022]
Abstract
DNA fingerprinting, one of the great discoveries of the late 20th century, has revolutionized forensic investigations. This review briefly recapitulates 30 years of progress in forensic DNA analysis which helps to convict criminals, exonerate the wrongly accused, and identify victims of crime, disasters, and war. Current standard methods based on short tandem repeats (STRs) as well as lineage markers (Y chromosome, mitochondrial DNA) are covered and applications are illustrated by casework examples. Benefits and risks of expanding forensic DNA databases are discussed and we ask what the future holds for forensic DNA fingerprinting.
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Affiliation(s)
- Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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Mundorff A, Davoren JM. Examination of DNA yield rates for different skeletal elements at increasing post mortem intervals. Forensic Sci Int Genet 2013; 8:55-63. [PMID: 24315589 DOI: 10.1016/j.fsigen.2013.08.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 11/28/2022]
Abstract
Identification of contemporary human remains by DNA STR testing is mainly limited by the ability to isolate sufficient amounts of DNA from the skeletal samples. A key part of this work relies on selection of the skeletal element with the best chance of obtaining a DNA STR profile. DNA was extracted from 55 bone samples, from 3 recently skeletonized individuals, representing most element types in the human body. Comparison of DNA yields from samples within an individual showed that the small cancellous bones on average have much higher amounts of DNA per unit mass than dense cortical bones. Complete 16 locus STR profiles were obtained for all 3 individuals from 36 of the element types, 10 had full profiles for 2 of the 3 individuals, 3 had full profiles for 1 of the 3 and 5 did not have any full profiles. The sample types with the least STR loci were from the arms. Ten skeletal elements were tested from 12 additional skeletons ranging from 3-21 years post mortem interval (PMI). At increasing PMI the small cancellous bones continued to yield more DNA and STR loci than the cortical bones. These findings suggest that the current recommendation for selection of long cortical bone samples for DNA testing of skeletal remains should be re-evaluated.
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Affiliation(s)
- Amy Mundorff
- Department of Anthropology, The University of Tennessee, 250 South Stadium Hall, Knoxville, TN 37996, USA
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Parker LS, London AJ, Aronson JD. Incidental findings in the use of DNA to identify human remains: an ethical assessment. Forensic Sci Int Genet 2012; 7:221-9. [PMID: 23116722 DOI: 10.1016/j.fsigen.2012.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/02/2012] [Accepted: 10/05/2012] [Indexed: 11/28/2022]
Abstract
DNA analysis is increasingly used to identify the remains of victims of conflicts and disasters. This is especially true in cases where remains are badly damaged and fragmented, or where antemortem records are unavailable. Incidental findings (IFs)-that is, genetics-related information for which investigators were not looking-may result from these identification efforts employing DNA analysis. Because of the critical role played by family members of the missing in identification efforts, as well as the familial nature of DNA, identification initiatives employing DNA analysis are particularly prone to reveal IFs about familial relationships, such as misattributed paternity or false beliefs about sibling relationships. Despite forensic scientists' widespread awareness of the possibility of generating IFs, to date there has been relatively little explicit guidance about their management. This paper fills that gap. It offers substantive guidance about the ethical management of IFs in this context. To ensure that the analysis addresses actual needs and practices in the field, one author (JDA) conducted semi-structured interviews with key informants from six regionally diverse organizations involved in post-conflict or post-disaster identification efforts. The paper first describes how methods of DNA analysis give rise to IFs. Next, it explains the importance of developing an ethically justified general policy for managing IFs and discusses features of DNA identification efforts that are relevant to such a policy. Then it presents an argument in support of a general policy of nondisclosure-specifically, that considerations of fair access to the individual and social benefits of identification efforts, and the concern to minimize and fairly distribute the risks of participation, support a policy of nondisclosure. It concludes by considering some implications of this argument for the choice among scientific practices involved in using DNA analysis to identify human remains, as well as for managing non-genetic incidental findings.
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Affiliation(s)
- Lisa S Parker
- Center for Bioethics and Health Law, University of Pittsburgh, Pittsburgh, PA 15213, United States.
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Abstract
The amplification of short tandem repeat (STR) markers throughout the human nuclear DNA genome are used to associate crime scene evidence to the perpetrator's profile in criminal investigations. For highly challenged or compromised materials such as stains exposed to the elements, skeletal remains from missing persons cases, or fragmented and degraded samples from mass disasters, obtaining a full STR profile may be difficult if not impossible. With the introduction of short amplicon STR or "miniSTR" typing, it is possible to obtain STR genetic information from highly challenged samples without the need to sequence the hypervariable regions of the mitochondrial DNA (mtDNA) genome. Non-Combined DNA Index System (CODIS) STR markers have been developed to obtain information beyond the core CODIS loci. This chapter will focus on the steps necessary to prepare and use one of the non-CODIS (NC) multiplexes, NC01 (Coble and Butler 2005), for analysis on capillary electrophoresis instrumentation.
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48
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Abstract
Forensic DNA testing has a number of applications, including parentage testing, identifying human remains from natural or man-made disasters or terrorist attacks, and solving crimes. This article provides background information followed by an overview of the process of forensic DNA testing, including sample collection, DNA extraction, PCR amplification, short tandem repeat (STR) allele separation and sizing, typing and profile interpretation, statistical analysis, and quality assurance. The article concludes with discussions of possible problems with the data and other forensic DNA testing techniques.
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49
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Montelius K, Lindblom B. DNA analysis in Disaster Victim Identification. Forensic Sci Med Pathol 2011; 8:140-7. [PMID: 22009165 DOI: 10.1007/s12024-011-9276-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2011] [Indexed: 10/16/2022]
Abstract
DNA profiling and matching is one of the primary methods to identify missing persons in a disaster, as defined by the Interpol Disaster Victim Identification Guide. The process to identify a victim by DNA includes: the collection of the best possible ante-mortem (AM) samples, the choice of post-mortem (PM) samples, DNA-analysis, matching and statistical weighting of the genetic relationship or match. Each disaster has its own scenario, and each scenario defines its own methods for identification of the deceased.
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Affiliation(s)
- Kerstin Montelius
- National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology, Artillerigatan 12, 587 58, Linköping, Sweden.
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50
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Bradford L, Heal J, Anderson J, Faragher N, Duval K, Lalonde S. Disaster victim investigation recommendations from two simulated mass disaster scenarios utilized for user acceptance testing CODIS 6.0. Forensic Sci Int Genet 2011; 5:291-6. [DOI: 10.1016/j.fsigen.2010.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 05/06/2010] [Accepted: 05/15/2010] [Indexed: 10/19/2022]
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