1
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Emery MV, Bolhofner K, Spake L, Ghafoor S, Versoza CJ, Rawls EM, Winingear S, Buikstra JE, Loreille O, Fulginiti LC, Stone AC. Targeted enrichment of whole-genome SNPs from highly burned skeletal remains. J Forensic Sci 2024; 69:1558-1577. [PMID: 38415845 DOI: 10.1111/1556-4029.15482] [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: 09/29/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality and quantity using next-generation sequencing (NGS). We present whole-genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed-effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole-genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures <350°C are the most likely sources for higher genomic DNA yields. Furthermore, we observed an inverse correlation between the number of captured SNPs and the extent to which samples were burned, as well as a significant decrease in the total number of SNPs measured for samples subjected to temperatures >350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.
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Affiliation(s)
- Matthew V Emery
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Katelyn Bolhofner
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
- School of Interdisciplinary Forensics, Arizona State University, Glendale, Arizona, USA
| | - Laure Spake
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Suhail Ghafoor
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Cyril J Versoza
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Erin M Rawls
- School of Life Sciences, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Stevie Winingear
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Jane E Buikstra
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
| | - Odile Loreille
- FBI Laboratory, DNA Support Unit, Quantico, Virginia, USA
| | - Laura C Fulginiti
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Maricopa County Office of the Medical Examiner, Phoenix, Arizona, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
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2
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Liu X, Yang C, Chen X, Han X, Liu H, Zhang X, Xu Q, Yang X, Liu C, Chen L, Liu C. A novel 193-plex MPS panel integrating STRs and SNPs highlights the application value of forensic genetics in individual identification and paternity testing. Hum Genet 2024; 143:371-383. [PMID: 38499885 DOI: 10.1007/s00439-024-02658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
Massively parallel sequencing (MPS) has emerged as a promising technology for targeting multiple genetic loci simultaneously in forensic genetics. Here, a novel 193-plex panel was designed to target 28 A-STRs, 41 Y-STRs, 21 X-STRs, 3 sex-identified loci, and 100 A-SNPs by employing a single-end 400 bp sequencing strategy on the MGISEQ-2000™ platform. In the present study, a series of validations and sequencing of 1642 population samples were performed to evaluate the overall performance of the MPS-based panel and its practicality in forensic application according to the SWGDAM guidelines. In general, the 193-plex markers in our panel showed good performance in terms of species specificity, stability, and repeatability. Compared to commercial kits, this panel achieved 100% concordance for standard gDNA and 99.87% concordance for 14,560 population genotypes. Moreover, this panel detected 100% of the loci from 0.5 ng of DNA template and all unique alleles at a 1:4 DNA mixture ratio (0.2 ng minor contributor), and the applicability of the proposed approach for tracing and degrading DNA was further supported by case samples. In addition, several forensic parameters of STRs and SNPs were calculated in a population study. High CPE and CPD values greater than 0.9999999 were clearly demonstrated and these results could be useful references for the application of this panel in individual identification and paternity testing. Overall, this 193-plex MPS panel has been shown to be a reliable, repeatable, robust, inexpensive, and powerful tool sufficient for forensic practice.
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Affiliation(s)
- Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Chengliang Yang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Xiaohui Chen
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, Guangdong, 510030, China
| | - Xiaolong Han
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, Guangdong, 510030, China
| | - Hong Liu
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, Guangdong, 510030, China
| | - Xingkun Zhang
- DeepReads Biotech, Guangzhou, Guangdong, 510000, China
| | - Quyi Xu
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, Guangdong, 510030, China
| | - Xingyi Yang
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, Guangdong, 510030, China
| | - Changhui Liu
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, Guangdong, 510030, China.
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, Guangdong, 510230, China.
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3
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Kayser M, Sajantila A, Butler JM, Parson W, Salas A, Gill P, Parsons T, Phillips C, Egeland T, Marshall C. Special issue: Forensic Genetics: Unde venisti et quo vadis? Forensic Sci Int Genet 2023:102881. [PMID: 37173159 DOI: 10.1016/j.fsigen.2023.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, the Netherland.
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki and Finnish Institute for Health and Welfare, Helsinki, Finland
| | - John M Butler
- National Institute of Standards and Technology, Special Programs Office, Gaithersburg, MD, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Austria and Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Antonio Salas
- Forensic Genetics Unit, Institute of Forensic Sciences and GenPoB Research Group, Institute of Health Research, Clinic Hospital, University of Santiago de Compostela, Spain
| | - Peter Gill
- Forensic Genetics Research Group, Oslo University Hospital and Department of Clinical Medicine, University of Oslo, Norway
| | - Thomas Parsons
- International Commission on Missing Persons, Den Haag, the Netherlands
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Thore Egeland
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Charla Marshall
- Emerging Technologies Section, Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE, USA
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4
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Watherston J, McNevin D. Skull and long bones – Forensic DNA techniques for historic shipwreck human remains. AUST J FORENSIC SCI 2023. [DOI: 10.1080/00450618.2023.2181395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- J. Watherston
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
- Biology Unit, Forensic Science Branch, Nt Police, Fire and Emergency Services, Berrimah, NT, Australia
- College of Health & Human Sciences, Faculty of Science, Charles Darwin University, Casuarina, NT, Australia
| | - D. McNevin
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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5
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Bolarín JM, Pérez-Cárceles M, Luna A, Minguela A, Muro M, Legaz I. Killer cell immunoglobulin-like receptors (KIR) genes can be an adequate tool in forensic anthropological studies: evaluation in a wide Caucasian Spanish population. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.1930156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- J. M. Bolarín
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - M.D. Pérez-Cárceles
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - A. Luna
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - A. Minguela
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - M. Muro
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - I. Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
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6
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The analysis of ancestry with small-scale forensic panels of genetic markers. Emerg Top Life Sci 2021; 5:443-453. [PMID: 33949669 DOI: 10.1042/etls20200327] [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: 02/03/2021] [Revised: 04/07/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022]
Abstract
In the last 10 years, forensic genetic analysis has been extended beyond identification tests that link a suspect to crime scene evidence using standard DNA profiling, to new supplementary tests that can provide information to investigators about a suspect in the absence of a database hit or eyewitness testimony. These tests now encompass the prediction of physical appearance, ancestry and age. In this review, we give a comprehensive overview of the full range of DNA-based ancestry inference tests designed to work with forensic contact traces, when the level of DNA is often very low or highly degraded. We outline recent developments in the design of ancestry-informative marker sets, forensic assays that use capillary electrophoresis or massively parallel sequencing, and the statistical analysis frameworks that examine the test profile and compares it to reference population variation. Three casework ancestry analysis examples are described which were successfully accomplished in the authors' laboratory, where the ancestry information obtained was critical to the outcome of the DNA analyses made.
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7
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Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu SF. Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software. Genes (Basel) 2021; 12:genes12040599. [PMID: 33921728 PMCID: PMC8073089 DOI: 10.3390/genes12040599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
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8
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Mckinnon M, Higgins D. Comparison of bone demineralisation procedures for DNA recovery from burned remains. Forensic Sci Int Genet 2020; 51:102448. [PMID: 33373911 DOI: 10.1016/j.fsigen.2020.102448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/09/2020] [Accepted: 12/01/2020] [Indexed: 11/26/2022]
Abstract
Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.
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Affiliation(s)
- Meghan Mckinnon
- 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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9
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Cho S, Kim MY, Lee JH, Lee HY, Lee SD. Large-scale identification of human bone remains via SNP microarray analysis with reference SNP database. Forensic Sci Int Genet 2020; 47:102293. [PMID: 32276230 DOI: 10.1016/j.fsigen.2020.102293] [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: 05/25/2019] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are valuable markers complementary to conventional forensic short tandem repeat (STR) markers in genetic typing, with potential advantages in challenging forensic casework. With the advent of high-throughput technologies, such as microarrays and massively parallel sequencing, the use of SNP typing has now expanded to large-scale forensic applications. Herein, a forensic case is presented to demonstrate the usefulness of SNP typing in identifying large-scale human bone remains with reference database construction. A total of 402 bone remains were recovered from an island in the Jeju Province of Korea where a massive disaster occurred in 1948. The first phase of the identification process was accomplished via conventional DNA typing methods including autosomal and Y-chromosomal STR typing, and mitochondrial DNA sequencing, which resulted in the identification of 74 of 402 remains. The second phase of the identification involved the remaining 327 unidentified remains using SNP typing as a supplementary tool based on Affymetrix resequencing array. The SNP markers of 782 family members were also analyzed and a reference database was constructed for comparison. An additional 51 bone remains were identified in the second phase. SNP data obtained from the supplementary genotyping yielded additional genetic information as well as contributed to kinship testing to determine the second degrees of relationship. In addition SNPs are useful in discriminating ambiguous relationship when only STR data are available. A software program developed for SNP typing system enabled efficient kinship analysis for large-scale forensic identification. The results and the casework are described and discussed.
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Affiliation(s)
- Sohee Cho
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Moon-Young Kim
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Hwan Young Lee
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Soong Deok Lee
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea.
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10
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Kaur S, Saini V, Dalal R. UV-Visible spectroscopic effect on Haemoglobin & DNA degradation: A forensic approach. Forensic Sci Int 2020; 307:110078. [PMID: 31923852 DOI: 10.1016/j.forsciint.2019.110078] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/30/2019] [Accepted: 11/23/2019] [Indexed: 11/17/2022]
Abstract
In forensic casework, sample degradation is a largely an unsolved problem that exists due to poor preservation protocols. In Indian subcontinent, the forensic blood stains are commonly exposed to different ecological conditions for months before they are collected and transferred to the forensic laboratory for analysis. Under such conditions, the question of haemoglobin (Hb) & nucleic acid stability is of utmost importance. The biological evidence, especially the blood sample that underwent extreme conditions should further be retained in an appropriate storage facility until processed for the forensic serology/DNA testing. The present study provides the spectroscopic approach of analyzing Hb and DNA degradation of forensic blood samples preserved under varied conditions (tabulated and graphically). These samples were further subjected to and DNA analysis to assess the quality of sample based on different preservation conditions. At last, this study suggests the effective and appropriate preservation protocol of sample soon after its collection.
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Affiliation(s)
- Suminder Kaur
- Regional Forensic Science Laboratory, DNA Fingerprinting Unit, Biology Division, New Delhi 110021, India.
| | - Vineeta Saini
- Department of Forensic Sciences, Faculty of Sciences, SGT University, Gurugram, Haryana, India.
| | - Ritika Dalal
- Regional Forensic Science Laboratory, DNA Fingerprinting Unit, Biology Division, New Delhi 110021, India.
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11
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Gaudio D, Fernandes DM, Schmidt R, Cheronet O, Mazzarelli D, Mattia M, O'Keeffe T, Feeney RNM, Cattaneo C, Pinhasi R. Genome-Wide DNA from Degraded Petrous Bones and the Assessment of Sex and Probable Geographic Origins of Forensic Cases. Sci Rep 2019; 9:8226. [PMID: 31160682 PMCID: PMC6547751 DOI: 10.1038/s41598-019-44638-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/09/2019] [Indexed: 12/21/2022] Open
Abstract
The acquisition of biological information and assessment of the most probable geographic origin of unidentified individuals for obtaining positive identification is central in forensic sciences. Identification based on forensic DNA, however, varies greatly in relation to degradation of DNA. Our primary aim is to assess the applicability of a petrous bone sampling method in combination with Next Generation Sequencing to evaluate the quality and quantity of DNA in taphonomically degraded petrous bones from forensic and cemetery cases. A related aim is to analyse the genomic data to obtain the molecular sex of each individual, and their most probable geographic origin. Six of seven subjects were previously identified and used for comparison with the results. To analyse their probable geographic origin, samples were genotyped for the 627.719 SNP positions. Results show that the inner ear cochlear region of the petrous bone provides good percentages of endogenous DNA (14.61–66.89%), even in the case of burnt bodies. All comparisons between forensic records and genetic results agree (sex) and are compatible (geographic origin). The application of the proposed methodology may be a powerful tool for use in forensic scenarios, ranging from missing persons to unidentified migrants who perish when crossing borders.
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Affiliation(s)
- Daniel Gaudio
- School of Archaeology and Earth Institute, University College of Dublin, Dublin 4, Belfield, Ireland.
| | - Daniel M Fernandes
- School of Archaeology and Earth Institute, University College of Dublin, Dublin 4, Belfield, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14 1090, Wien, Austria.,CIAS, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Ryan Schmidt
- School of Archaeology and Earth Institute, University College of Dublin, Dublin 4, Belfield, Ireland
| | - Olivia Cheronet
- School of Archaeology and Earth Institute, University College of Dublin, Dublin 4, Belfield, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14 1090, Wien, Austria
| | - Debora Mazzarelli
- LabAnOF, Sezione di Medicina Legale, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 37, 20133, Milano, Italy
| | - Mirko Mattia
- LabAnOF, Sezione di Medicina Legale, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 37, 20133, Milano, Italy
| | - Tadhg O'Keeffe
- School of Archaeology and Earth Institute, University College of Dublin, Dublin 4, Belfield, Ireland
| | - Robin N M Feeney
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin 4, Belfield, Ireland
| | - Cristina Cattaneo
- LabAnOF, Sezione di Medicina Legale, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 37, 20133, Milano, Italy
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14 1090, Wien, Austria.
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12
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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13
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Bose N, Carlberg K, Sensabaugh G, Erlich H, Calloway C. Target capture enrichment of nuclear SNP markers for massively parallel sequencing of degraded and mixed samples. Forensic Sci Int Genet 2018. [DOI: 10.1016/j.fsigen.2018.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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14
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Parys-Proszek A, Wróbel M, Marcińska M, Kupiec T. Dual amplification strategy for improved efficiency of forensic DNA analysis using NGM Detect™, NGM™ or Globalfiler™ kits. Forensic Sci Int Genet 2018; 35:46-49. [PMID: 29635120 DOI: 10.1016/j.fsigen.2018.03.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/15/2018] [Accepted: 03/30/2018] [Indexed: 11/15/2022]
Abstract
The new generation of STR amplification kits with improved sensitivity and additional genetic markers is designed particularly for analyzing difficult traces with a high DNA degradation index, presence of inhibitors and low level of DNA. In the new NGM Detect™ kit, modifications including changing the primers' sequences and shortening of STR markers are introduced. The quality control system (IQCS, IQCL) used to detect DNA degradation and the presence of inhibitors in the sample is an additional feature. The purpose of this study was to compare the results of analysis of different kinds of typical casework samples obtained using NGM™ or GlobalFiler™ kits with those generated using the new NGM Detect™ kit. The results indicate that the tested kit is particularly useful for the analysis of challenging samples for which incomplete profiles are generated with the NGM™ or GlobalFiler™ kits. The increased number of positively typed alleles gives better statistical parameters in genetic identification cases. We conclude that the NGM Detect™ kit can be recommended for the double amplification protocol together with the NGM or GlobalFiler™ kits.
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Affiliation(s)
- Agnieszka Parys-Proszek
- Institute of Forensic Research, Forensic Genetics Section, Westerplatte St. 9, Kraków, Poland
| | - Maria Wróbel
- Institute of Forensic Research, Forensic Genetics Section, Westerplatte St. 9, Kraków, Poland
| | - Magdalena Marcińska
- Institute of Forensic Research, Forensic Genetics Section, Westerplatte St. 9, Kraków, Poland
| | - Tomasz Kupiec
- Institute of Forensic Research, Forensic Genetics Section, Westerplatte St. 9, Kraków, Poland.
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15
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Set up of cutoff thresholds for kinship determination using SNP loci. Forensic Sci Int Genet 2017; 29:1-8. [DOI: 10.1016/j.fsigen.2017.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 03/04/2017] [Accepted: 03/06/2017] [Indexed: 12/20/2022]
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Evaluation of the Qiagen 140-SNP forensic identification multiplex for massively parallel sequencing. Forensic Sci Int Genet 2017; 28:35-43. [DOI: 10.1016/j.fsigen.2017.01.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 01/21/2023]
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17
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Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review. Int J Legal Med 2016; 131:21-37. [DOI: 10.1007/s00414-016-1490-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/31/2016] [Indexed: 10/20/2022]
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Cho S, Seo HJ, Lee J, Yu HJ, Lee SD. Kinship Testing Based on SNPs Using Microarray System. Transfus Med Hemother 2016; 43:429-432. [PMID: 27994531 DOI: 10.1159/000446322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/15/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Kinship testing using biallelic SNP markers has been demonstrated to be a promising approach as a supplement to standard STR typing, and several systems, such as pyrosequencing and microarray, have been introduced and utilized in real forensic cases. The Affymetrix microarray containing 169 autosomal SNPs developed for forensic application was applied to our practical case for kinship analysis that had remained inconclusive due to partial STR profiles of degraded DNA and possibility of inbreeding within the population. CASE REPORT 169 autosomal SNPs were typed on array with severely degraded DNA of two bone samples, and the kinship compared to genotypes in a reference database of their putative family members. RESULTS Two bone samples remained unidentified through traditional STR typing with partial profiles of 10 or 14 of 16 alleles. Because these samples originated from a geographically isolated population, a cautious approach was required when analyzing and declaring true paternity only based on PI values. In a supplementary SNP typing, 106 and 78 SNPs were obtained, and the match candidates were found in each case with improved PI values than using only STRs and with no discrepant SNPs in comparison. CONCLUSION Our case showed that the utility of multiple SNPs on array is expected in practical forensic caseworks with an establishment of reference database.
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Affiliation(s)
- Sohee Cho
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Hee Jin Seo
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Jihyun Lee
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Hyung Jin Yu
- DNA Link, Seoul, South Korea, Seoul, South Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea; Institute of Forensic Science, Seoul National University, College of Medicine, Seoul, South Korea
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19
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De Angelis D, Gibelli D, Palazzo E, Sconfienza L, Obertova Z, Cattaneo C. Skeletal idiopathic osteosclerosis helps to perform personal identification of unknown decedents: A novel contribution from anatomical variants through CT scan. Sci Justice 2016; 56:260-3. [PMID: 27320398 DOI: 10.1016/j.scijus.2016.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/16/2016] [Accepted: 03/24/2016] [Indexed: 10/22/2022]
Abstract
Personal identification consists of the comparison of ante-mortem information from a missing person with post-mortem data obtained from an unidentified corpse. Such procedure is based on the assessment of individualizing features which may help in providing a conclusive identification between ante-mortem and post-mortem material. Anatomical variants may provide important clues to correctly identify human remains. Areas of idiopathic osteosclerosis (IO), or dense bone islands (DBIs) characterized by radiopaque areas of dense, trabeculated, non-inflamed vital bone represent one of these, potentially individualizing, anatomical features. This study presents a case where the finding of DBI was crucial for a positive identification through CT-scan. A decomposed body was found in an apartment in June 2014 in advanced decomposition and no dental records were available to perform a comparison for positive identification. Genetic tests were not applicable because of the lack of relatives in a direct line. The analysis of the only ante-mortem documentation, a CT-scan to the deceased dating back to August 2009, showed the presence of three DBIs within the trabecular bone of the proximal portion of the right femur. The same bony district was removed from the corpse during the autopsy and analysed by CT-scan, which verified the presence of the same features. Forensic practitioners should therefore be aware of the great importance of anatomical bone variants, such as dense bone islands for identification purposes, and the importance of advanced radiological technique for addressing the individualizing potential of such variants. We propose that anatomical variants of the human skeleton should be considered as being "primary identification characteristics" similar to dental status, fingerprints and DNA.
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Affiliation(s)
- D De Angelis
- LABANOF, Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy
| | - D Gibelli
- LABANOF, Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy.
| | - E Palazzo
- LABANOF, Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy
| | - L Sconfienza
- Dipartimento di Radiologia, IRCCS Ospedale San Donato, Milano, Italy
| | - Z Obertova
- LABANOF, Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy
| | - C Cattaneo
- LABANOF, Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy
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20
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Use of ancestry-informative markers as a scientific tool to combat the illegal traffic in human kidneys. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Factors influencing the reliability of DNA typing results for bone samples. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Braganholi D, Polverari F, Ambrosio I, Cicarelli R. Insertion of amelogenin marker in the 38 Hid-Indels multiplex reaction. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Pontes ML, Fondevila M, Laréu MV, Medeiros R. SNP Markers as Additional Information to Resolve Complex Kinship Cases. Transfus Med Hemother 2015; 42:385-8. [PMID: 26733770 DOI: 10.1159/000440832] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/31/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND DNA profiling with sets of highly polymorphic autosomal short tandem repeat (STR) markers has been applied in various aspects of human identification in forensic casework for nearly 20 years. However, in some cases of complex kinship investigation, the information provided by the conventionally used STR markers is not enough, often resulting in low likelihood ratio (LR) calculations. In these cases, it becomes necessary to increment the number of loci under analysis to reach adequate LRs. Recently, it has been proposed that single nucleotide polymorphisms (SNPs) could be used as a supportive tool to STR typing, eventually even replacing the methods/markers now employed. METHODS In this work, we describe the results obtained in 7 revised complex paternity cases when applying a battery of STRs, as well as 52 human identification SNPs (SNPforID 52plex identification panel) using a SNaPshot methodology followed by capillary electrophoresis. RESULTS Our results show that the analysis of SNPs, as complement to STR typing in forensic casework applications, would at least increase by a factor of 4 total PI values and correspondent Essen-Möller's W value. CONCLUSIONS We demonstrated that SNP genotyping could be a key complement to STR information in challenging casework of disputed paternity, such as close relative individualization or complex pedigrees subject to endogamous relations.
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Affiliation(s)
- M Lurdes Pontes
- Laboratório de Genética e Biologia Forenses, National Institute of Legal Medicine and Forensic Sciences, North Delegation, Porto, Portugal; CENCIFOR- Forensic Science Center, Porto, Portugal
| | - Manuel Fondevila
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria Victoria Laréu
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Rui Medeiros
- Molecular Oncology, Portuguese Institute of Oncology, Porto, Portugal; ICBAS, Abel Salazar Institute for the Biomedical Sciences, University of Porto, Porto, Portugal; LPCC, Research Department-Portuguese League Against Cancer (NRNorte), Porto, Portugal
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24
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Santos C, Fondevila M, Ballard D, Banemann R, Bento AM, Børsting C, Branicki W, Brisighelli F, Burrington M, Capal T, Chaitanya L, Daniel R, Decroyer V, England R, Gettings KB, Gross TE, Haas C, Harteveld J, Hoff-Olsen P, Hoffmann A, Kayser M, Kohler P, Linacre A, Mayr-Eduardoff M, McGovern C, Morling N, O'Donnell G, Parson W, Pascali VL, Porto MJ, Roseth A, Schneider PM, Sijen T, Stenzl V, Court DS, Templeton JE, Turanska M, Vallone PM, Oorschot RAHV, Zatkalikova L, Carracedo Á, Phillips C. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise. Forensic Sci Int Genet 2015; 19:56-67. [PMID: 26122263 DOI: 10.1016/j.fsigen.2015.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/06/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.
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Affiliation(s)
- C Santos
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M Fondevila
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - D Ballard
- Department of Forensic and Analytical Science, Faculty of Life Science, King's College London, UK
| | - R Banemann
- Federal Criminal Police Office, Wiesbaden, Germany
| | - A M Bento
- Forensic Genetic and Biology Service, Centre Branch, National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen, Denmark
| | - W Branicki
- Section of Forensic Genetics, Institute of Forensic Research, Kraków, Poland
| | - F Brisighelli
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - T Capal
- Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - L Chaitanya
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - R Daniel
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia
| | - V Decroyer
- National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, Brussels, Belgium
| | - R England
- ESR, Private Bag 92021, Auckland, New Zealand
| | - K B Gettings
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - T E Gross
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - C Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - J Harteveld
- Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands
| | - P Hoff-Olsen
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - A Hoffmann
- Federal Criminal Police Office, Wiesbaden, Germany
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - P Kohler
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - A Linacre
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia
| | - M Mayr-Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - C McGovern
- ESR, Private Bag 92021, Auckland, New Zealand
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen, Denmark; National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, Brussels, Belgium
| | - G O'Donnell
- Forensic Science Laboratory, Dublin, Ireland
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - V L Pascali
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - M J Porto
- Forensic Genetic and Biology Service, Centre Branch, National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - A Roseth
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - T Sijen
- Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands
| | - V Stenzl
- Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - D Syndercombe Court
- Department of Forensic and Analytical Science, Faculty of Life Science, King's College London, UK
| | - J E Templeton
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia
| | - M Turanska
- Institute of Forensic Science, Ministry of the Interior, Department of Biology and DNA Analysis, Slovenská Lupca, Slovakia
| | - P M Vallone
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - R A H van Oorschot
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia
| | - L Zatkalikova
- Institute of Forensic Science, Ministry of the Interior, Department of Biology and DNA Analysis, Slovenská Lupca, Slovakia
| | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
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25
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Pontes ML, Medeiros R. Autosomal SNPs in different forensic applications. AUST J FORENSIC SCI 2015. [DOI: 10.1080/00450618.2015.1050067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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De Angelis D, Gibelli D, Gaudio D, Cipriani Noce F, Guercini N, Varvara G, Sguazza E, Sforza C, Cattaneo C. Sexual dimorphism of canine volume: A pilot study. Leg Med (Tokyo) 2015; 17:163-6. [DOI: 10.1016/j.legalmed.2014.12.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/05/2014] [Accepted: 12/11/2014] [Indexed: 11/27/2022]
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27
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Development of a novel miniplex DNA identification system for the Japanese population. Leg Med (Tokyo) 2015; 17:205-9. [PMID: 25596639 DOI: 10.1016/j.legalmed.2014.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/31/2014] [Accepted: 12/16/2014] [Indexed: 11/24/2022]
Abstract
To aid DNA identification using 36 short tandem repeat (STR) loci for kinship analysis, likelihood ratio (LR) distributions were estimated using the allele frequency data evaluated for the Japanese population in our previous study. The results revealed that the LR tended to be higher when kinship analysis was performed using the 36 STR loci than when the analysis was performed using Identifiler®, the most commonly used commercial DNA typing kit in Japan, even when a sibship case was analyzed. However, a typing kit targeting 36 STR loci is not suitable for the analysis of damaged DNA. In this study, we developed a novel miniplex DNA identification system targeting 7 STR loci (D3S1744, D5S818, D8S1179, D10S2325, Penta D, Penta E, and vWA) that was optimized for use in combination with MiniFiler™ for the Japanese population. The combined matching probability of the MiniFiler plus miniplex system was 4.8×10(-19), which is lower than that of Identifiler (4.3×10(-17)). All expected alleles were detected successfully on DNA isolated from HepG2 human hepatocarcinoma cells by the miniplex system, but no significant signal was observed from a DNA sample isolated from COS-7 African green monkey kidney cells.
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28
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Romanini C, Romero M, Salado Puerto M, Catelli L, Phillips C, Pereira R, Gusmão L, Vullo C. Ancestry informative markers: inference of ancestry in aged bone samples using an autosomal AIM-Indel multiplex. Forensic Sci Int Genet 2014; 16:58-63. [PMID: 25531060 DOI: 10.1016/j.fsigen.2014.11.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 10/25/2014] [Accepted: 11/28/2014] [Indexed: 01/22/2023]
Abstract
Ancestry informative markers (AIMs) can be useful to infer ancestry proportions of the donors of forensic evidence. The probability of success typing degraded samples, such as human skeletal remains, is strongly influenced by the DNA fragment lengths that can be amplified and the presence of PCR inhibitors. Several AIM panels are available amongst the many forensic marker sets developed for genotyping degraded DNA. Using a 46 AIM Insertion Deletion (Indel) multiplex, we analyzed human skeletal remains of post mortem time ranging from 35 to 60 years from four different continents (Sub-Saharan Africa, South and Central America, East Asia and Europe) to ascertain the genetic ancestry components. Samples belonging to non-admixed individuals could be assigned to their corresponding continental group. For the remaining samples with admixed ancestry, it was possible to estimate the proportion of co-ancestry components from the four reference population groups. The 46 AIM Indel set was informative enough to efficiently estimate the proportion of ancestry even in samples yielding partial profiles, a frequent occurrence when analyzing inhibited and/or degraded DNA extracts.
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Affiliation(s)
- Carola Romanini
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Magdalena Romero
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Mercedes Salado Puerto
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Laura Catelli
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, Faculty of Medicine, University of Santiago de Compostela, ES-15705 Santiago de Compostela, Galicia, Spain
| | - Rui Pereira
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Leonor Gusmão
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Carlos Vullo
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina.
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29
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Phillips C, Parson W, Lundsberg B, Santos C, Freire-Aradas A, Torres M, Eduardoff M, Børsting C, Johansen P, Fondevila M, Morling N, Schneider P, Carracedo Á, Lareu M. Building a forensic ancestry panel from the ground up: The EUROFORGEN Global AIM-SNP set. Forensic Sci Int Genet 2014; 11:13-25. [DOI: 10.1016/j.fsigen.2014.02.012] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 02/12/2014] [Accepted: 02/17/2014] [Indexed: 11/16/2022]
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30
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Torres SRR, Uehara CJS, Sutter-Latorre AF, de Almeida BS, Sauerbier TS, Muniz YCN, Marrero AR, de Souza IR. Population genetic data and forensic parameters of 30 autosomal InDel markers in Santa Catarina State population, Southern Brazil. Mol Biol Rep 2014; 41:5429-33. [DOI: 10.1007/s11033-014-3414-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 05/13/2014] [Indexed: 10/25/2022]
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Hou G, Jiang X, Yang Y, Jia F, Li Q, Zhao J, Guo F, Liu L. A 21-locus autosomal SNP multiplex and its application in forensic science. J Forensic Sci 2013; 59:5-14. [PMID: 24400826 DOI: 10.1111/1556-4029.12259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 08/06/2012] [Accepted: 10/14/2012] [Indexed: 02/06/2023]
Abstract
To develop a cost-effective technique for single-nucleotide polymorphism (SNP) genotyping and improve the efficiency to analyze degraded DNA, we have established a novel multiplex system including 21-locus autosomal SNPs and amelogenin locus, which was based on allele-specific amplification (ASA) and universal reporter primers (URP). The target amplicons for each of the 21 SNPs arranged from 63 base pair (bp) to 192 bp. The system was tested in 539 samples from three ethnic groups (Han, Mongolian, and Zhuang population) in China, and the total power of discrimination (TPD) and cumulative probability of exclusion (CPE) were more than 0.99999999 and 0.98, respectively. The system was further validated with forensic samples and full profiles could be achieved from degraded DNA and 63 case-type samples. In summary, the multiplex system offers an effective technique for individual identification of forensic samples and is much more efficient in the analysis of degraded DNA compared with standard STR typing.
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Affiliation(s)
- Guangwei Hou
- Department of Forensic DNA, Criminal Science and Technology Institute of Liaoning province, Shenyang, 110032, China
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Comparison of the genetic background of different Colombian populations using the SNPforID 52plex identification panel. Int J Legal Med 2013; 128:19-25. [PMID: 23665814 DOI: 10.1007/s00414-013-0858-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 03/28/2013] [Indexed: 12/17/2022]
Abstract
Various strategies for analysing SNP markers and genotyping have been published with the goal of obtaining informative profiles from biological samples that contain only small amounts of template and/or degraded DNA. In this study, a multiplex assay of 52 autosomal single-nucleotide polymorphisms (SNPs) was used to analyse 438 individuals from urban populations from different regions of Colombia, as well as a sample of 50 Native American individuals of the Pastos ethnic group from Nariño. To determine if significant differences in these 52 SNPs exist between the distinct regions of Colombia, genetic distance and admixture analyses were performed based on the available data for 17 different Colombian population groups and for population groups from Africa, Europe and America. The results demonstrate significant differences between the populations from the Southwest Andean, Central-West Andean, Central-East Andean, Orinoquian and northern Colombian Pacific Coast regions. Most of the regions exhibited a European and Native American admixture. One exception is the population from the region of Chocó (on the northern Pacific Coast), which exhibits a high proportion of African admixture (54 %). From the observed genetic backgrounds, it is possible to conclude that a single reference database for the entire country would not be suitable for forensic purposes. The allele frequencies and the forensically relevant parameters were calculated for all of the markers in each Colombian region with significant values for the combined matching probability (power of discrimination ≥0.99999999999999990) and the combined probability of exclusion (≥0.9990) in trios that were obtained from all of the population groups.
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33
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Zaumsegel D, Rothschild MA, Schneider PM. A 21 marker insertion deletion polymorphism panel to study biogeographic ancestry. Forensic Sci Int Genet 2013; 7:305-12. [PMID: 23352554 DOI: 10.1016/j.fsigen.2012.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/21/2012] [Accepted: 12/26/2012] [Indexed: 11/19/2022]
Abstract
Insertion/deletion polymorphisms have recently received increased interest in the forensic genetics community. This class of markers combines the advantageous genetic properties of single nucleotide polymorphisms (i.e., low mutation rate, genetic stability, and short amplicon size) with the technical advantage of short tandem repeat markers (simple detection by fluorescence-labelled PCR and capillary electrophoresis). For a large number of indel markers significant differences in allele frequencies between the major populations have been reported, making this class of markers suitable for the analysis of biogeographic ancestry. We have developed a multiplex PCR assay designed to establish the biogeographic ancestry of forensic DNA samples based on insertion/deletion polymorphisms. A panel of 21 short indels with allele frequency differences between three major population groups (European, African and Asian) was selected to be incorporated into a single-tube multiplex PCR assay. The assay is highly sensitive, requiring less than 0.5 ng of genomic DNA for successful typing. Due to the short fragment lengths below 200 bp, the assay is ideally suited for the typing of challenging forensic genetic case work samples. A population genetic study has been performed proving the performance of the assay in inferring the ancestral population of individuals. The chosen 21 markers are sufficient to distinguish between three major global population groups. Furthermore, the assay design leaves room for an extension in order to cover additional population groups.
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Affiliation(s)
- Daniel Zaumsegel
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Köln, Germany.
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Ruiz Y, Chiurillo M, Borjas L, Phillips C, Lareu M, Carracedo Á. Analysis of the SNPforID 52-plex markers in four Native American populations from Venezuela. Forensic Sci Int Genet 2012; 6:e142-5. [DOI: 10.1016/j.fsigen.2012.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
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Barbaro A, Phillips C, Fondevila M, Lareu M, Carracedo A. Genetic variability of the SNPforID 52-plex identification SNP panel in Italian population samples. Forensic Sci Int Genet 2012; 6:e185-6. [PMID: 22840855 DOI: 10.1016/j.fsigen.2012.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/03/2012] [Accepted: 07/06/2012] [Indexed: 10/28/2022]
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36
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Fondevila M, Phillips C, Santos C, Freire Aradas A, Vallone PM, Butler JM, Lareu MV, Carracedo A. Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies. Forensic Sci Int Genet 2012; 7:63-74. [PMID: 22749789 DOI: 10.1016/j.fsigen.2012.06.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/28/2012] [Accepted: 06/07/2012] [Indexed: 01/15/2023]
Abstract
A revision of an established 34 SNP forensic ancestry test has been made by swapping the under-performing rs727811 component SNP with the highly informative rs3827760 that shows a near-fixed East Asian specific allele. We collated SNP variability data for the revised SNP set in 66 reference populations from 1000 Genomes and HGDP-CEPH panels and used this as reference data to analyse four U.S. populations showing a range of admixture patterns. The U.S. Hispanics sample in particular displayed heterogeneous values of co-ancestry between European, Native American and African contributors, likely to reflect in part, the way this disparate group is defined using cultural as well as population genetic parameters. The genotyping of over 700 U.S. population samples also provided the opportunity to thoroughly gauge peak mobility variation and peak height ratios observed from routine use of the single base extension chemistry of the 34-plex test. Finally, the genotyping of the widely used DNA profiling Standard Reference Material samples plus other control DNAs completes the audit of the 34-plex assay to allow forensic practitioners to apply this test more readily in their own laboratories.
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Affiliation(s)
- M Fondevila
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain
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37
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Forensic performance of two insertion–deletion marker assays. Int J Legal Med 2012; 126:725-37. [DOI: 10.1007/s00414-012-0721-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 05/21/2012] [Indexed: 01/15/2023]
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38
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Phillips C, García-Magariños M, Salas A, Carracedo A, Lareu MV. SNPs as Supplements in Simple Kinship Analysis or as Core Markers in Distant Pairwise Relationship Tests: When Do SNPs Add Value or Replace Well-Established and Powerful STR Tests? Transfus Med Hemother 2012; 39:202-210. [PMID: 22851936 DOI: 10.1159/000338857] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/03/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND: Genetic tests for kinship testing routinely reach likelihoods that provide virtual proof of the claimed relationship by typing microsatellites-commonly consisting of 12-15 standard forensic short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) have also been applied to kinship testing but these binary markers are required in greater numbers than multiple-allele STRs. However SNPs offer certain advantageous characteristics not found in STRs, including, much higher mutational stability, good performance typing highly degraded DNA, and the ability to be readily up-scaled to very high marker numbers reaching over a million loci. This article outlines kinship testing applications where SNPs markedly improve the genetic data obtained. In particular we explore the minimum number of SNPs that will be required to confirm pairwise relationship claims in deficient pedigrees that typify missing persons' identification or war grave investigations where commonly few surviving relatives are available for comparison and the DNA is highly degraded. METHODS: We describe the application of SNPs alongside STRs when incomplete profiles or allelic instability in STRs create ambiguous results, we review the use of high density SNP arrays when the relationship claim is very distant, and we outline simulations of kinship analyses with STRs supplemented with SNPs in order to estimate the practical limit of pairwise relationships that can be differentiated from random unrelated pairs from the same population. RESULTS: The minimum number of SNPs for robust statistical inference of parent-offspring relationships through to those of second cousins (S-3-3) is estimated for both simple, single multiplex SNP sets and for subsets of million-SNP arrays. CONCLUSIONS: There is considerable scope for resolving ambiguous STR results and for improving the statistical power of kinship analysis by adding small-scale SNP sets but where the pedigree is deficient the pairwise relationships must be relatively close. For more distant relationships it is possible to reduce chip-based SNP arrays from the million+ markers down to ∼7,000. However, such numbers indicate that current genotyping approaches will not be able to deliver sufficient data to resolve distant pairwise relationships from the limited DNA typical of the most challenging identification cases.
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Affiliation(s)
- Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Galicia, Spain
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Børsting C, Tomas C, Morling N. Typing of 49 autosomal SNPs by single base extension and capillary electrophoresis for forensic genetic testing. Methods Mol Biol 2012; 830:87-107. [PMID: 22139655 DOI: 10.1007/978-1-61779-461-2_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
We describe a method for simultaneous amplification of 49 autosomal single nucleotide polymorphisms (SNPs) by multiplex PCR and detection of the SNP alleles by single base extension (SBE) and capillary electrophoresis. All the SNPs may be amplified from only 100 pg of genomic DNA and the length of the amplicons range from 65 to 115 bp. The high sensitivity and the short amplicon sizes make the assay very suitable for typing of degraded DNA samples, and the low mutation rate of SNPs makes the assay very useful for relationship testing. Combined, these advantages make the assay well suited for disaster victim identifications, where the DNA from the victims may be highly degraded and the victims are identified via investigation of their relatives. The assay was validated according to the ISO 17025 standard and used for routine case work in our laboratory.
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Affiliation(s)
- Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
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Li S, Feng T, Fu L, Li Z, Lou C, Zhang X, Ma C, Cong B. Pyrosequencing of a short fragment of the amelogenin gene for gender identification. Mol Biol Rep 2012; 39:6949-57. [DOI: 10.1007/s11033-012-1522-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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Abstract
Ancestry inference based on autosomal markers remains a niche approach in forensic analysis: most laboratories feel more secure with a review of the cumulative STR profile frequencies in a range of relevant populations with the possible additional analysis of mitochondrial and/or Y-chromosome variability. However, a proportion of autosomal single nucleotide polymorphisms (SNPs) show very well-differentiated allele frequencies among global population-groups. Furthermore, such ancestry informative marker SNPs (AIM-SNPs) lend themselves to relatively straightforward typing with short-amplicon PCR and multiplexed single base extension reactions using the same capillary electrophoresis detectors required for the sequencing and STR genotyping of mainstream forensic markers. In this chapter, we describe a 34 AIM-SNP multiplex that is robust enough for the analysis of challenging, often highly degraded DNA typical of much of routine forensic casework. We also outline in detail the in-silico procedures necessary for collecting parental population reference data from the SPSmart SNP databases and performing ancestry inference of single AIM-SNP profiles or large-scale population data using the companion ancestry analysis website of Snipper. Two casework examples are described that show, in both cases, that an inference of likely ancestry using AIM-SNPs helped the identification of highly degraded skeletal material.
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Capillary electrophoresis of human mtDNA control region sequences from highly degraded samples using short mtDNA amplicons. Methods Mol Biol 2012; 830:283-99. [PMID: 22139668 DOI: 10.1007/978-1-61779-461-2_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The forensic applications of mtDNA sequencing center primarily on samples that are either highly degraded or contain little or no nuclear DNA, since the testing of these sample types is often unsuccessful with more widely used nuclear STR profiling assays. In these cases, sequence data from the noncoding mtDNA control region are targeted due to its high variability. However, the ease of authentic DNA recovery and the strategy used for recovery depend strictly on the quality of the sample. In this chapter, we will cover mitochondrial DNA sequencing procedures for short mtDNA amplicons which range in size from 100 to 350 bp. Generally speaking, amplicons of this size are required only for the most degraded specimens, and the protocols described here have been specifically developed for recalcitrant human skeletal remains encountered during the course of a large-scale missing persons' identification effort. DNA templates from these types of specimens tend to exhibit various forms of intrastrand damage that, in turn, manifest as artifacts in the sequence data. Because these artifacts are not generally observed among sequence data from pristine templates, we address the particular data idiosyncrasies that warrant additional scrutiny. Although this chapter will primarily highlight this particular application, the basic experimental parameters and data considerations should easily extend to other applications and/or sample types. The protocols described here have been deliberately designed to produce raw sequence electropherograms and final mtDNA profiles that adhere to the strictest forensic guidelines in terms of overall data quality.
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Comparison of Identifiler®, Identifiler Plus® and Minifiler® performance in an initial paternity testing study on old skeletal remains at the forensic and legal medicine area of the Government of Andorra (Pyrenees). FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Soler M, Silva M, Guimarães M, Sousa M, Stilhano R, Han S, Iwamura E. STR analysis in bones exposed to Brazilian tropical climate. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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45
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Freire-Aradas A, Fondevila M, Kriegel AK, Phillips C, Gill P, Prieto L, Schneider PM, Carracedo A, Lareu MV. A new SNP assay for identification of highly degraded human DNA. Forensic Sci Int Genet 2011; 6:341-9. [PMID: 21908243 DOI: 10.1016/j.fsigen.2011.07.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 11/28/2022]
Abstract
There is growing evidence that the histone-DNA complexes found in nucleosomes offer protection from DNA degradation processes, including apoptotic events in addition to bacterial and environmental degradation. We sought to locate human nucleosome regions and build a catalogue of SNPs sited near the middle of these genomic segments that could be combined into a single PCR multiplex specifically for use with extremely degraded human genomic DNA samples. Using recently optimized bio-informatics tools for the reliable identification of nucleosome sites based on sequence motifs and their positions relative to known promoters, 1395 candidate loci were collected to construct an 18-plex single base extension assay. Genotyping performance of the nucleosome SNPs was tested using artificially degraded DNA and 24 casework samples where the likely state of degradation of DNA was established by comparison to profile completeness in four other forensic assays: a standard 15-plex STR identification test, a miniaturized STR multiplex and two autosomal SNP multiplexes. The nucleosome SNP assay gave genotyping success rates 6% higher than the best existing forensic SNP assay: the SNPforID Auto-2 29-plex and significantly higher than the mini-STR assay. The nucleosome SNPs we located and combined therefore provide a new type of marker set that can be used to supplement existing approaches when the analysed DNA is likely to be extremely degraded and may fail to give sufficient STR genotypes for a reliable identification.
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Affiliation(s)
- A Freire-Aradas
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain
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Børsting C, Tomas C, Morling N. SNP typing of the reference materials SRM 2391b 1–10, K562, XY1, XX74, and 007 with the SNPforID multiplex. Forensic Sci Int Genet 2011; 5:e81-2. [DOI: 10.1016/j.fsigen.2010.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 11/25/2022]
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47
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Application of mtDNA SNP analysis in forensic casework. Forensic Sci Int Genet 2011; 5:216-21. [DOI: 10.1016/j.fsigen.2010.01.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 12/18/2009] [Accepted: 01/24/2010] [Indexed: 10/19/2022]
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48
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Santos C, Phillips C, Fondevila M, Porras-Hurtado L, Carracedo A, Souto L, Lareu MV. A study of East Timor variability using the SNPforID 52-plex SNP panel. Forensic Sci Int Genet 2011; 5:e25-6. [PMID: 20457102 DOI: 10.1016/j.fsigen.2010.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Revised: 03/15/2010] [Accepted: 03/15/2010] [Indexed: 11/19/2022]
Abstract
A set of 52 autosomal single nucleotide polymorphism (SNP) loci was analyzed in 46 unrelated individuals from the East Timor population using the forensic assay previously described by Sanchez et al. (2006) [J.J. Sanchez, C. Phillips, C. Børsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe Court, PM. Schneider, A. Carracedo, N. Morling, A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis 27 (2006) 1713-1724]. Allele frequencies are presented for the 52 SNPs with all loci in Hardy-Weinberg equilibrium for the study population. Comparison with African, European, East Asian and Oceanian populations of the CEPH human genome diversity panel (CEPH-HGDP) revealed significant differences in allele frequency distributions between East Timor and each of the above population groups. Statistical parameters measuring forensic informativeness were also calculated and the values obtained reached comparable levels to those previously described for the other global population groups. This is the first study of variability in these SNPs in an Oceanian population outside of the CEPH-HGDP.
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Affiliation(s)
- C Santos
- Forensic Genetics Department, University of Santiago de Compostela, Hospital Clínico Universitario, Galicia, Spain
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Schwark T, Heinrich A, Preusse-Prange A, von Wurmb-Schwark N. Reliable genetic identification of burnt human remains. Forensic Sci Int Genet 2010; 5:393-9. [PMID: 20832378 DOI: 10.1016/j.fsigen.2010.08.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 07/05/2010] [Accepted: 08/12/2010] [Indexed: 11/18/2022]
Abstract
The identification of severely burnt human remains by genetic fingerprinting is a common task in forensic routine work. In cases of extreme fire impact, only hard tissues (bones, teeth) may be left for DNA analysis. DNA extracted from burnt bone fragments may be highly degraded, making an amplification of genetic markers difficult or even impossible. Furthermore, heavily burnt bones are very prone to contamination with external DNA. We investigated whether authentic DNA profiles can be generated from human bones showing different stages of fire induced destruction (well preserved, semi-burnt, black burnt, blue-grey burnt, blue-grey-white burnt). DNA was extracted from 71 bone fragments derived from 13 individuals. Obtained genetic patterns (STRs and mtDNA sequences) were compared to the genetic pattern of the respective bodies. Our results show that the identification via DNA analysis is reliably and reproducibly possible from well preserved and semi-burnt bones. In black burnt bones the DNA was highly degraded and in some cases no nuclear DNA was left, leaving mitochondrial DNA analysis as an option. Blue-grey burnt bones lead only sporadically to authentic profiles. The investigation of blue-grey-white burnt bones barely led to reliable results.
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Affiliation(s)
- Thorsten Schwark
- Department of Legal Medicine, Christian-Albrechts-University of Kiel, Arnold-Heller-Str. 12, 24105 Kiel, Germany.
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Ancestry analysis in the 11-M Madrid bomb attack investigation. PLoS One 2009; 4:e6583. [PMID: 19668368 PMCID: PMC2719087 DOI: 10.1371/journal.pone.0006583] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 07/08/2009] [Indexed: 11/26/2022] Open
Abstract
The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR) profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA) and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP) assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48). Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs) that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The results achieved illustrate the benefit of adding specialized marker sets to provide enhanced scope and power to an already highly effective system of DNA analysis for forensic identification.
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