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Panneerchelvam S, Norazmi MN. DNA Profiling in Human Identification: From Past to Present. Malays J Med Sci 2023; 30:5-21. [PMID: 38239252 PMCID: PMC10793127 DOI: 10.21315/mjms2023.30.6.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/02/2022] [Indexed: 01/22/2024] Open
Abstract
Forensic DNA typing has been widely accepted in the courts all over the world. This is because DNA profiling is a very powerful tool to identify individuals on the basis of their unique genetic makeup. DNA evidence is capable of not only identifying the presence of specific biospecimens in a crime scene, but it is also used to exonerate suspects who are innocent of a crime. Technological advancements in DNA profiling, including the development of validated kits and statistical methods have made this tool to be more precise in forensic investigations. Therefore, validated combined DNA index system (CODIS) short tandem repeats (STRs) kits which require very small amount of DNA, coupled with real-time polymerase chain reaction (PCR) and the statistical strengths are used routinely to identify human remains, establish paternity or to match suspected crime scene biospecimens. The road to modern DNA profiling has been long, and it has taken scientists decades of work and fine tuning to develop highly accurate testing and analyses that are used today. This review will discuss the various DNA polymorphisms and their utility in human identity testing.
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Affiliation(s)
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
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2
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Vanichanukulyakit J, Khacha-ananda S, Monum T, Mahawong P, Moophayak K, Penkhrue W, Khumpook T, Thongsahuan S. The Analysis of Genetic Polymorphism on Mitochondrial Hypervariable Region III in Thai Population. Genes (Basel) 2023; 14:genes14030682. [PMID: 36980954 PMCID: PMC10048634 DOI: 10.3390/genes14030682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Mitochondrial DNA (mtDNA) analysis is a genetic marker for human identification, especially matrilineal inheritance. Hypervariable regions (HVR) I and II of mtDNA have been currently performed for human identification worldwide. Further examination of HVRIII has been conducted with the aim of enhancing the power of discrimination. The aim of this research is to provide informative data on the polymorphisms of HVRIII in the Thai population in order to establish a national database for human identification. Thai people who were unrelated through the maternal lineage were recruited for blood collections. The mtDNA was extracted by Chelex extraction, amplified by polymerase chain reaction, and analyzed using Sequencing Analysis Software. The most common mutation in HVRIII was base substitution, followed by deletion and insertion. We discovered 40 unique haplotypes, with haplotype 489C being the most frequent. The haplotype diversity, power of discrimination, and random match probability were 0.8014, 0.7987, and 0.2013, respectively. Five-CA repeats were the most frequently observed in nucleotide positions 514–523. Our database can be employed as supplementary markers in addition to nuclear deoxyribonucleic acid (DNA) markers in forensic investigations. Moreover, the data could potentially enhance genetic identification and anthropological genetics research in Thailand.
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Affiliation(s)
- Jirat Vanichanukulyakit
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | - Supakit Khacha-ananda
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, 239, Huay Kaew Road, Muang, Chiang Mai 50200, Thailand
- Correspondence:
| | - Tawachai Monum
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | - Phatcharin Mahawong
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | | | - Watsana Penkhrue
- School of Preclinic, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Taddaow Khumpook
- Faculty of Science at Sriracha, Kasetsart University, Sriracha Campus, Chonburi 20230, Thailand;
| | - Sorawat Thongsahuan
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand;
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3
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Lutz-Bonengel S, Niederstätter H, Naue J, Koziel R, Yang F, Sänger T, Huber G, Berger C, Pflugradt R, Strobl C, Xavier C, Volleth M, Weiß SC, Irwin JA, Romsos EL, Vallone PM, Ratzinger G, Schmuth M, Jansen-Dürr P, Liehr T, Lichter P, Parsons TJ, Pollak S, Parson W. Evidence for multi-copy Mega-NUMTs in the human genome. Nucleic Acids Res 2021; 49:1517-1531. [PMID: 33450006 PMCID: PMC7897518 DOI: 10.1093/nar/gkaa1271] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022] Open
Abstract
The maternal mode of mitochondrial DNA (mtDNA) inheritance is central to human genetics. Recently, evidence for bi-parental inheritance of mtDNA was claimed for individuals of three pedigrees that suffered mitochondrial disorders. We sequenced mtDNA using both direct Sanger and Massively Parallel Sequencing in several tissues of eleven maternally related and other affiliated healthy individuals of a family pedigree and observed mixed mitotypes in eight individuals. Cells without nuclear DNA, i.e. thrombocytes and hair shafts, only showed the mitotype of haplogroup (hg) V. Skin biopsies were prepared to generate ρ° cells void of mtDNA, sequencing of which resulted in a hg U4c1 mitotype. The position of the Mega-NUMT sequence was determined by fluorescence in situ hybridization and two different quantitative PCR assays were used to determine the number of contributing mtDNA copies. Thus, evidence for the presence of repetitive, full mitogenome Mega-NUMTs matching haplogroup U4c1 in various tissues of eight maternally related individuals was provided. Multi-copy Mega-NUMTs mimic mixtures of mtDNA that cannot be experimentally avoided and thus may appear in diverse fields of mtDNA research and diagnostics. We demonstrate that hair shaft mtDNA sequencing provides a simple but reliable approach to exclude NUMTs as source of misleading results.
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Affiliation(s)
- Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Jana Naue
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Rafal Koziel
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck 6020, Austria
| | - Fengtang Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Timo Sänger
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - René Pflugradt
- State Investigation Department of Lower Saxony, Hannover 30169, Germany
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Marianne Volleth
- Magdeburg University Hospital, Institute of Human Genetics, Otto von Guericke University, Magdeburg 39120, Germany
| | - Sandra Carina Weiß
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, Quantico, VA 22135, USA
| | - Erica L Romsos
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, MD 20899, USA
| | - Peter M Vallone
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, MD 20899, USA
| | - Gudrun Ratzinger
- Department of Dermatology, Venereology and Allergy, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Matthias Schmuth
- Department of Dermatology, Venereology and Allergy, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Pidder Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck 6020, Austria
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena 07747, Germany
| | - Peter Lichter
- German Cancer Research Center, Molecular Genetics, Heidelberg 69120, Germany
| | - Thomas J Parsons
- International Commission on Missing Persons, The Hague 2514 AA, Netherlands
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stefan Pollak
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
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4
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Bright JA, Kelly H, Kerr Z, McGovern C, Taylor D, Buckleton JS. The interpretation of forensic DNA profiles: an historical perspective. J R Soc N Z 2019. [DOI: 10.1080/03036758.2019.1692044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Jo-Anne Bright
- Forensic Business Group, Institute of Environmental Science and Research Limited, Auckland, New Zealand
| | - Hannah Kelly
- Forensic Business Group, Institute of Environmental Science and Research Limited, Auckland, New Zealand
| | - Zane Kerr
- Forensic Business Group, Institute of Environmental Science and Research Limited, Auckland, New Zealand
| | - Catherine McGovern
- Forensic Business Group, Institute of Environmental Science and Research Limited, Auckland, New Zealand
| | - Duncan Taylor
- Forensic Biology Group, Forensic Science South Australia, Adelaide, Australia
| | - John S. Buckleton
- Forensic Business Group, Institute of Environmental Science and Research Limited, Auckland, New Zealand
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5
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Desmyter S, Dognaux S, Noel F, Prieto L. Base specific variation rates at mtDNA positions 16093 and 16183 in human hairs. Forensic Sci Int Genet 2019; 43:102142. [PMID: 31437782 DOI: 10.1016/j.fsigen.2019.102142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
Abstract
Small variations between haplotypes detected in different tissues from the same individual have been previously described. These differences complicate the interpretation of mtDNA results in real forensic casework. mtDNA haplotypes detected in hair strands collected at the crime scene have to be frequently compared with haplotypes of reference samples (buccal swabs) from victims or suspects. Nucleotide position 16093 is a well-known hot spot where differences can accumulate between different tissues of the same individual. Intra individual variation was also detected at positions 16182 and 16183 in haplotypes showing an uninterrupted HV1 poly-C stretch (with 16189C). In order to better characterize the type of variation in these positions between buccal cells and hair strands from the same individual, we have performed Sanger sequencing in 25-28 hair strands (411 in total) from 15 individuals showing either an uninterrupted HV1 polyC-stretch (16189C) or 16093C/Y in their buccal cells. The results have been evaluated by also taking into account our previous results published in [19]. We have found that no variation among hair strands was detected in individuals showing T16093 in buccal cells, while variation in hair strands (T16093, 16093C and 16093Y) were detected in individuals showing 16093C or 16093Y in buccal cells. Regarding nucleotide positions 16182 and 16183 in combination with an uninterrupted polyC-stretch, no variation was detected in hairs from individuals showing A16182 16183C in their buccal cells. In contrast, individuals A16182 A16183 showed hair strands with A16182 16183 M and A16182 16183C. And finally, individuals with 16182C 16183C showed some variation in a small amount of their hair strands (some hairs with 16182 M 16183C). These results can be relevant for forensic practitioners when comparing reference samples with hair strands, which is the type of sample most tested by using mtDNA analysis in forensic casework.
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Affiliation(s)
- Stijn Desmyter
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium.
| | - Sophie Dognaux
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Fabrice Noel
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Lourdes Prieto
- Instituto de Ciencias Forenses. Grupo de Medicina Xenómica. Universidade de Santiago de Compostela, Spain; Laboratorio ADN. Comisaría General de Policía Científica, Madrid, Spain
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6
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Pilli E, Boccone S, Agostino A, Virgili A, D'Errico G, Lari M, Rapone C, Barni F, Moggi Cecchi J, Berti A, Caramelli D. From unknown to known: Identification of the remains at the mausoleum of fosse Ardeatine. Sci Justice 2018; 58:469-478. [DOI: 10.1016/j.scijus.2018.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/08/2018] [Accepted: 05/20/2018] [Indexed: 11/26/2022]
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7
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Huber N, Parson W, Dür A. Next generation database search algorithm for forensic mitogenome analyses. Forensic Sci Int Genet 2018; 37:204-214. [PMID: 30241075 DOI: 10.1016/j.fsigen.2018.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) variation is being reported relative to the corrected version of the first sequenced human mitochondrial genome. A review of the existing literature across disciplines that employ mtDNA demonstrates that insertions and deletions are not reported in a standardized way. This may lead to false exclusions of identical sequences, unidentified matches in missing persons mtDNA databases, biased mtDNA database frequency estimates and overestimation of the genetic evidence. Seven years ago we introduced alignment-free database search software (SAM) and implemented it into the mtDNA database EMPOP (https://empop.online) to produce reliable and conservative frequency estimates that are required in the forensic context. However, ambiguity remained in how laboratories have been reporting mitotypes, as often more than one single alignment of a given mtDNA sequence was feasible. In order to overcome this limitation we here describe a concept and provide software for producing stable, harmonized phylogenetic alignment of mtDNA sequences for database searches. The new software SAM 2 will be made available via EMPOP and provide the user with the already established conservative frequency estimates. In addition, SAM 2 offers the rCRS-coded haplotype of a given mtDNA sequence following the established and widely accepted phylogenetic alignment. This provides the user with feedback on how mitotypes are stored in EMPOP and how they should be reported in order to harmonize nomenclature. Finally, this approach does not only permit reliable mtDNA nomenclature in forensics but invites related disciplines to take advantage of a standardized way of reporting mtDNA variation, thus closing the ranks between different genetic fields and supporting dialogue and collaboration between mtDNA scholars from various disciplines.
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Affiliation(s)
- Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
| | - Arne Dür
- Institute of Mathematics, University of Innsbruck, Austria
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8
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Zupanič Pajnič I, Petaros A, Balažic J, Geršak K. Searching for the mother missed since the Second World War. J Forensic Leg Med 2016; 44:138-142. [DOI: 10.1016/j.jflm.2016.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/07/2016] [Accepted: 10/22/2016] [Indexed: 10/20/2022]
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9
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Estimation and Preparation of the Hypervariable Regions I/II Templates for Mitochondrial DNA Typing From Human Bones and Teeth Remains Using Singleplex Quantitative Polymerase Chain Reaction. Am J Forensic Med Pathol 2016; 37:158-64. [DOI: 10.1097/paf.0000000000000246] [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]
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10
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Abstract
In recent years the recovery and analysis of DNA from skeletal remains has been applied to several contexts ranging from disaster victim identification to the identification of the victims of conflict. Here are described procedures for processing the bone and tooth samples including mechanical and chemical cleaning, cutting and powdering in the presence of liquid nitrogen, complete demineralization of bone and tooth powder, DNA extraction, DNA purification using magnetic beads, and the precautions and strategies implemented to avoid and detect contamination. It has proven highly successful in the analysis of bones and teeth from Second World War victims' skeletal remains that have been excavated from mass graves in Slovenia and is also suitable for genetic identification of relatively fresh human remains.
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Affiliation(s)
- Irena Zupanič Pajnič
- Laboratory of Molecular Genetics, Institute of Forensic Medicine, Vrazov trg 2, 1104, Ljubljana, Slovenia.
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11
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TEZEL A, ÇETİNKAYA Ö, GÜZELTEPE B, KILIÇ N. Genetic identification with heteroplasmic variations in maternally relatedindividuals in forensic cases. Turk J Biol 2016. [DOI: 10.3906/biy-1506-62] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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12
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Abstract
The analysis of mitochondrial DNA (mtDNA) is an established forensic tool and has been used extensively to aid with both the identification of human remains and evidence recovered from scenes of crime. The biology of mtDNA confers both advantages and disadvantages when using it as a tool for identification. It benefits from a high copy number, which facilitates analysis from samples with highly degraded DNA or trace amounts of DNA, but the maternal mode of inheritance restricts its power of discrimination. With Next Generation Sequencing being used in research and some forensic casework laboratories the scope of mtDNA analysis in forensic casework may expand in the near future. Currently, however, most casework laboratories rely on Sanger sequencing and an established method for analyzing the hypervariable sequence regions is described.
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Affiliation(s)
- David Ballard
- Faculty of Life Sciences and Medicine, King's College London, Franklin Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK.
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13
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Genetic portrait of Lisboa immigrant population from Cabo Verde with mitochondrial DNA analysis. J Genet 2015; 94:509-12. [PMID: 26440093 DOI: 10.1007/s12041-015-0552-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Kareem MA, Abdulzahra AI, Hameed IH, Jebor MA. A new polymorphic positions discovered in mitochondrial DNA hypervariable region HVIII from central and north-central of Iraq. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3250-4. [DOI: 10.3109/19401736.2015.1007369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | | | - Imad Hadi Hameed
- Department of Molecular Biology, Babylon University, Hilla City, Iraq
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15
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Davis C, Peters D, Warshauer D, King J, Budowle B. Sequencing the hypervariable regions of human mitochondrial DNA using massively parallel sequencing: Enhanced data acquisition for DNA samples encountered in forensic testing. Leg Med (Tokyo) 2014; 17:123-7. [PMID: 25459369 DOI: 10.1016/j.legalmed.2014.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 10/03/2014] [Accepted: 10/05/2014] [Indexed: 11/19/2022]
Abstract
Mitochondrial DNA testing is a useful tool in the analysis of forensic biological evidence. In cases where nuclear DNA is damaged or limited in quantity, the higher copy number of mitochondrial genomes available in a sample can provide information about the source of a sample. Currently, Sanger-type sequencing (STS) is the primary method to develop mitochondrial DNA profiles. This method is laborious and time consuming. Massively parallel sequencing (MPS) can increase the amount of information obtained from mitochondrial DNA samples while improving turnaround time by decreasing the numbers of manipulations and more so by exploiting high throughput analyses to obtain interpretable results. In this study 18 buccal swabs, three different tissue samples from five individuals, and four bones samples from casework were sequenced at hypervariable regions I and II using STS and MPS. Sample enrichment for STS and MPS was PCR-based. Library preparation for MPS was performed using Nextera® XT DNA Sample Preparation Kit and sequencing was performed on the MiSeq™ (Illumina, Inc.). MPS yielded full concordance of base calls with STS results, and the newer methodology was able to resolve length heteroplasmy in homopolymeric regions. This study demonstrates short amplicon MPS of mitochondrial DNA is feasible, can provide information not possible with STS, and lays the groundwork for development of a whole genome sequencing strategy for degraded samples.
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Affiliation(s)
- Carey Davis
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Dixie Peters
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - David Warshauer
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Jonathan King
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
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16
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Lyons LA, Grahn RA, Kun TJ, Netzel LR, Wictum EE, Halverson JL. Acceptance of domestic cat mitochondrial DNA in a criminal proceeding. Forensic Sci Int Genet 2014; 13:61-7. [PMID: 25086413 DOI: 10.1016/j.fsigen.2014.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/20/2014] [Accepted: 07/07/2014] [Indexed: 02/06/2023]
Abstract
Shed hair from domestic animals readily adheres to clothing and other contact items, providing a source of transfer evidence for criminal investigations. Mitochondrial DNA is often the only option for DNA analysis of shed hair. Human mitochondrial DNA analysis has been accepted in the US court system since 1996. The murder trial of the State of Missouri versus Henry L. Polk, Jr. represents the first legal proceeding where cat mitochondrial DNA analysis was introduced into evidence. The mitochondrial DNA evidence was initially considered inadmissible due to concerns about the cat dataset and the scientific acceptance of the marker. Those concerns were subsequently addressed, and the evidence was deemed admissible. This report reviews the case in regards to the cat biological evidence and its ultimate admission as generally accepted and reliable. Expansion and saturation analysis of the cat mitochondrial DNA control region dataset supported the initial interpretation of the evidence.
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Affiliation(s)
- Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States.
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States; Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Teri J Kun
- Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Linda R Netzel
- Kansas City Police Crime Laboratory, 6633 Troost Avenue, Kansas City, MO 64131, United States
| | - Elizabeth E Wictum
- Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Joy L Halverson
- Zoogen Services, 1046 Olive Drive Suite 1, Davis, CA 95616, United States
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17
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Schwark T, Poetsch M, Modrow JH, Preuße-Prange A, von Wurmb-Schwark N. Nachweis von DNA-Spuren an Schneide- und Stichwerkzeugen. Rechtsmedizin (Berl) 2014. [DOI: 10.1007/s00194-014-0955-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics. Forensic Sci Int Genet 2014; 12:30-7. [PMID: 24879032 DOI: 10.1016/j.fsigen.2014.03.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 03/18/2014] [Accepted: 03/27/2014] [Indexed: 11/21/2022]
Abstract
RESULTS of sequencing of whole mitochondrial genome, HV1 and HV2 DNA with the second generation system (SGS) Roche 454 GS Junior were compared with results of Sanger sequencing and SNP typing with SNaPshot single base extension detected with MALDI-TOF and capillary electrophoresis. We investigated the performance of the software analysis of the data, reproducibility, ability to sequence homopolymeric regions, detection of mixtures and heteroplasmy as well as the implications of the depth of coverage. We found full reproducibility between samples sequenced twice with SGS. We found close to full concordance between the mtDNA sequences of 26 samples obtained with (1) the 454 SGS method using a depth of coverage above 100 and (2) Sanger sequencing and SNP typing. The discrepancies were primarily observed in homopolymeric regions. The 454 SGS method was able to sequence 95% of the reads correctly in homopolymers up to 4 bases, and up to 6 bases could be sequenced with similar success if the results were carefully, visually inspected. The 454 technology was able to detect mixtures or heteroplasmy of approximately 10%. We detected previously unreported heteroplasmy in the GM9947A component of the NIST human mitochondrial DNA SRM-2392 standard reference material.
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19
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Yang IS, Lee HY, Yang WI, Shin KJ. mtDNAprofiler: A Web Application for the Nomenclature and Comparison of Human Mitochondrial DNA Sequences,. J Forensic Sci 2013; 58:972-80. [DOI: 10.1111/1556-4029.12139] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 03/06/2012] [Accepted: 06/02/2012] [Indexed: 12/01/2022]
Affiliation(s)
- In Seok Yang
- Department of Forensic Medicine; Yonsei University College of Medicine; 50 Yonsei-ro, Seodaemun-gu; Seoul; 120-752; Korea
| | | | - Woo Ick Yang
- Department of Forensic Medicine; Yonsei University College of Medicine; 50 Yonsei-ro, Seodaemun-gu; Seoul; 120-752; Korea
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Wilson MR, Weaver SC, Winegar RA. Legal, technical, and interpretational considerations in the forensic analysis of viruses. J Forensic Sci 2013; 58:344-57. [PMID: 23406474 DOI: 10.1111/1556-4029.12065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 02/13/2012] [Accepted: 03/10/2012] [Indexed: 11/27/2022]
Abstract
The forensic evaluation of viruses presents new challenges to the forensic science community. Although many criminal cases have been adjudicated involving the deliberate transmission of viruses, especially HIV, this review provides a general approach to viral forensics, especially in light of significant biodefense challenges. Newly emerging techniques of nucleic acid sequencing are discussed in a forensic context. Human mitochondrial DNA analysis, wherein mixed profiles are routinely assessed in a forensic context, provides the groundwork for an interpretational approach to the issue of mixed DNA sequences. The importance of phylogenetic classification is discussed as both providing an integrated graphical depiction of the structure of viral nucleic acid variation as well as offering a tool that can be used to assess the relatedness of complex populations of nucleic acids.
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Affiliation(s)
- Mark R Wilson
- Forensic Science Program, Western Carolina University, 325 Natural Science Bldg, Cullowhee, NC, 28723
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21
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Kim NY, Lee HY, Park SJ, Yang WI, Shin KJ. Modified midi- and mini-multiplex PCR systems for mitochondrial DNA control region sequence analysis in degraded samples. J Forensic Sci 2013; 58:738-43. [PMID: 23406419 DOI: 10.1111/1556-4029.12062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 01/17/2012] [Accepted: 03/04/2012] [Indexed: 11/27/2022]
Abstract
Two multiplex polymerase chain reaction (PCR) systems (Midiplex and Miniplex) were developed for the amplification of the mitochondrial DNA (mtDNA) control region, and the efficiencies of the multiplexes for amplifying degraded DNA were validated using old skeletal remains. The Midiplex system consisted of two multiplex PCRs to amplify six overlapping amplicons ranging in length from 227 to 267 bp. The Miniplex system consisted of three multiplex PCRs to amplify 10 overlapping short amplicons ranging in length from 142 to 185 bp. Most mtDNA control region sequences of several 60-year-old and 400-500-year-old skeletal remains were successfully obtained using both PCR systems and consistent with those previously obtained by monoplex amplification. The multiplex system consisting of smaller amplicons is effective for mtDNA sequence analyses of ancient and forensic degraded samples, saving time, cost, and the amount of DNA sample consumed during analysis.
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Affiliation(s)
- Na Young Kim
- Department of Forensic Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-752, Korea
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22
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Calatayud M, Ramos A, Santos C, Aluja MP. Primer effect in the detection of mitochondrial DNA point heteroplasmy by automated sequencing. ACTA ACUST UNITED AC 2013; 24:303-11. [PMID: 23350969 DOI: 10.3109/19401736.2012.760072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The correct detection of mitochondrial DNA (mtDNA) heteroplasmy by automated sequencing presents methodological constraints. The main goals of this study are to investigate the effect of sense and distance of primers in heteroplasmy detection and to test if there are differences in the accurate determination of heteroplasmy involving transitions or transversions. A gradient of the heteroplasmy levels was generated for mtDNA positions 9477 (transition G/A) and 15,452 (transversion C/A). Amplification and subsequent sequencing with forward and reverse primers, situated at 550 and 150 bp from the heteroplasmic positions, were performed. Our data provide evidence that there is a significant difference between the use of forward and reverse primers. The forward primer is the primer that seems to give a better approximation to the real proportion of the variants. No significant differences were found concerning the distance at which the sequencing primers were placed neither between the analysis of transitions and transversions. The data collected in this study are a starting point that allows to glimpse the importance of the sequencing primers in the accurate detection of point heteroplasmy, providing additional insight into the overall automated sequencing strategy.
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Affiliation(s)
- Marta Calatayud
- Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
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23
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Mitochondrial DNA control region variation from samples of the Moroccan population. Int J Legal Med 2013; 127:757-9. [DOI: 10.1007/s00414-012-0813-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/17/2012] [Indexed: 11/27/2022]
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24
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Kjellström A, Edlund H, Lembring M, Ahlgren V, Allen M. An analysis of the alleged skeletal remains of Carin Göring. PLoS One 2012; 7:e44366. [PMID: 23284605 PMCID: PMC3526542 DOI: 10.1371/journal.pone.0044366] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 08/06/2012] [Indexed: 11/21/2022] Open
Abstract
In 1991, treasure hunters found skeletal remains in an area close to the destroyed country residence of former Nazi leader Hermann Göring in northeastern Berlin. The remains, which were believed to belong to Carin Göring, who was buried at the site, were examined to determine whether it was possible to make a positive identification. The anthropological analysis showed that the remains come from an adult woman. The DNA analysis of several bone elements showed female sex, and a reference sample from Carin's son revealed mtDNA sequences identical to the remains. The profile has one nucleotide difference from the Cambridge reference sequence (rCRS), the common variant 263G. A database search resulted in a frequency of this mtDNA sequence of about 10% out of more than 7,000 European haplotypes. The mtDNA sequence found in the ulna, the cranium and the reference sample is, thus, very common among Europeans. Therefore, nuclear DNA analysis was attempted. The remains as well as a sample from Carin's son were successfully analysed for the three nuclear markers TH01, D7S820 and D8S1179. The nuclear DNA analysis of the two samples revealed one shared allele for each of the three markers, supporting a mother and son relationship. This genetic information together with anthropological and historical files provides an additional piece of circumstantial evidence in our efforts to identify the remains of Carin Göring.
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Affiliation(s)
- Anna Kjellström
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Hanna Edlund
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Lembring
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktoria Ahlgren
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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25
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Holland MM, McQuillan MR, O'Hanlon KA. Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy. Croat Med J 2012; 52:299-313. [PMID: 21674826 PMCID: PMC3118725 DOI: 10.3325/cmj.2011.52.299] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Aim To use parallel array pyrosequencing to deconvolute mixtures of mitochondrial DNA (mtDNA) sequence and provide high resolution analysis of mtDNA heteroplasmy. Methods The hypervariable segment 1 (HV1) of the mtDNA control region was analyzed from 30 individuals using the 454 GS Junior instrument. Mock mixtures were used to evaluate the system’s ability to deconvolute mixtures and to reliably detect heteroplasmy, including heteroplasmic differences between 5 family members of the same maternal lineage. Amplicon sequencing was performed on polymerase chain reaction (PCR) products generated with primers that included multiplex identifiers (MID) and adaptors for pyrosequencing. Data analysis was performed using NextGENe® software. The analysis of an autosomal short tandem repeat (STR) locus (D18S51) and a Y-STR locus (DYS389 I/II) was performed simultaneously with a portion of HV1 to illustrate that multiplexing can encompass different markers of forensic interest. Results Mixtures, including heteroplasmic variants, can be detected routinely down to a component ratio of 1:250 (20 minor variant copies with a coverage rate of 5000 sequences) and can be readily detected down to 1:1000 (0.1%) with expanded coverage. Amplicon sequences from D18S51, DYS389 I/II, and the second half of HV1 were successfully partitioned and analyzed. Conclusions The ability to routinely deconvolute mtDNA mixtures down to a level of 1:250 allows for high resolution analysis of mtDNA heteroplasmy, and for differentiation of individuals from the same maternal lineage. The pyrosequencing approach results in poor resolution of homopolymeric sequences, and PCR/sequencing artifacts require a filtering mechanism similar to that for STR stutter and spectral bleed through. In addition, chimeric sequences from jumping PCR must be addressed to make the method operational.
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Affiliation(s)
- Mitchell M Holland
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16870, USA.
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26
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Sequence variation of mitochondrial DNA control region in North Central Venezuela. Forensic Sci Int Genet 2011; 6:e131-3. [PMID: 22189355 DOI: 10.1016/j.fsigen.2011.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 10/12/2011] [Accepted: 11/17/2011] [Indexed: 11/20/2022]
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27
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Forensic and genetic characterization of mtDNA from Pathans of Pakistan. Int J Legal Med 2010; 125:841-8. [PMID: 21184092 DOI: 10.1007/s00414-010-0540-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
Abstract
Complete mitochondrial control region data were generated for 230 unrelated Pathans from North West Frontier Province and Federally Administered Tribal Areas of Pakistan. To confirm data quality and to explore the genetic structure of Pathans, mitochondrial DNA haplogroup affiliation was determined by shared haplogroup-specific polymorphisms in the control region and by the analysis of diagnostic coding region single-nucleotide polymorphisms using a multiplex system for the assignment of eight haplogroups: M, N1'5, W, R, R0, T, J, and U. Sequence comparison revealed that 193 haplotypes were defined by 215 variable sites when major insertions were ignored at nucleotide positions 16193, 309, and 573. From a phylogenetic perspective, Pathans have a heterogeneous origin, displaying a high percentage of West Eurasian haplogroups followed by haplogroups native to South Asia and a small fraction from East Asian lineages. In population comparisons, this ethnic group differed significantly from several other ethnic groups from Pakistan and surrounding countries. These results suggest that frequency estimates for mtDNA haplotypes should be determined for endogamous ethnic groups individually instead of pooling data for these subpopulations into a single dataset for the Pakistani population. Data presented here may contribute to the accuracy of forensic mtDNA comparisons in the Pathans of Pakistan.
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Linacre A, Gusmão L, Hecht W, Hellmann AP, Mayr WR, Parson W, Prinz M, Schneider PM, Morling N. ISFG: recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations. Forensic Sci Int Genet 2010; 5:501-5. [PMID: 21106449 DOI: 10.1016/j.fsigen.2010.10.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 10/30/2010] [Indexed: 10/18/2022]
Abstract
The use of non-human DNA typing in forensic science investigations, and specifically that from animal DNA, is ever increasing. The term animal DNA in this document refers to animal species encountered in a forensic science examination but does not include human DNA. Non-human DNA may either be: the trade and possession of a species, or products derived from a species, which is contrary to legislation; as evidence where the crime is against a person or property; instances of animal cruelty; or where the animal is the offender. The first instance is addressed by determining the species present, and the other scenarios can often be addressed by assigning a DNA sample to a particular individual organism. Currently there is little standardization of methodologies used in the forensic analysis of animal DNA or in reporting styles. The recommendations in this document relate specifically to animal DNA that is integral to a forensic science investigation and are not relevant to the breeding of animals for commercial purposes. This DNA commission was formed out of discussions at the International Society for Forensic Genetics 23rd Congress in Buenos Aires to outline recommendations on the use of non-human DNA in a forensic science investigation. Due to the scope of non-human DNA typing that is possible, the remit of this commission is confined to animal DNA typing only.
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Affiliation(s)
- A Linacre
- School of Biology, Flinders University, Adelaide, Australia.
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29
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Tarditi CR, Grahn RA, Evans JJ, Kurushima JD, Lyons LA. Mitochondrial DNA sequencing of cat hair: an informative forensic tool. J Forensic Sci 2010; 56 Suppl 1:S36-46. [PMID: 21077873 DOI: 10.1111/j.1556-4029.2010.01592.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Approximately 81.7 million cats are in 37.5 million U.S. households. Shed fur can be criminal evidence because of transfer to victims, suspects, and/or their belongings. To improve cat hairs as forensic evidence, the mtDNA control region from single hairs, with and without root tags, was sequenced. A dataset of a 402-bp control region segment from 174 random-bred cats representing four U.S. geographic areas was generated to determine the informativeness of the mtDNA region. Thirty-two mtDNA mitotypes were observed ranging in frequencies from 0.6-27%. Four common types occurred in all populations. Low heteroplasmy, 1.7%, was determined. Unique mitotypes were found in 18 individuals, 10.3% of the population studied. The calculated discrimination power implied that 8.3 of 10 randomly selected individuals can be excluded by this region. The genetic characteristics of the region and the generated dataset support the use of this cat mtDNA region in forensic applications.
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Affiliation(s)
- Christy R Tarditi
- Department of Population Health and Reproduction, University of California, Davis, 95616, USA
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Röck A, Irwin J, Dür A, Parsons T, Parson W. SAM: String-based sequence search algorithm for mitochondrial DNA database queries. Forensic Sci Int Genet 2010; 5:126-32. [PMID: 21056022 PMCID: PMC3064999 DOI: 10.1016/j.fsigen.2010.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org).
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Affiliation(s)
- Alexander Röck
- Institute of Mathematics, University of Innsbruck, Technikerstrasse 13, 6020 Innsbruck, Austria
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Bovine mtDNA D-loop haplotypes exceed mutations in number despite reduced recombination: an effective alternative for identity control. Animal 2010; 4:1818-22. [PMID: 22445142 DOI: 10.1017/s1751731110001151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Mitochondrial (mt) DNA D-loop heterogeneity, haplotype distribution and possible sub-population structures within the relevant populations are important for DNA-based traceability. To gain insight into this distribution, we compared 1515 Bos taurus mtDNA D-loop sequences available from GenBank to 219 sequences that we sequenced de novo. A pronounced ambiguous trace typical of C-track length heteroplasmy was encountered in 5% of the samples, which were excluded from the analysis. Previously undescribed mutations and haplotypes were observed in 6% and 63% of the sequences, respectively. B. taurus haplotypes divided into the taurus, indicus and grunniens types and 302 variable sites formed the 858 taurus haplotypes detected. Fifty-five sites displayed a complex level of variation. As each level represents an independent mutation event, a total of 399 mutations were traced, which could potentially explain independent formation of less than half (47%) of the haplotypes encountered: most haplotypes were derived from different combinations of these mutations. We suggest that a mutational hotspot may explain these results and discuss the usefulness of mtDNA for identity and maternity assurance.
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Cardoso S, Zarrabeitia MT, Valverde L, Odriozola A, Alfonso-Sánchez MÁ, De Pancorbo MM. Variability of the Entire Mitochondrial DNA Control Region in a Human Isolate from the Pas Valley (Northern Spain). J Forensic Sci 2010; 55:1196-201. [DOI: 10.1111/j.1556-4029.2010.01440.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Parson W, Roewer L. Publication of population data of linearly inherited DNA markers in the International Journal of Legal Medicine. Int J Legal Med 2010; 124:505-9. [PMID: 20652581 DOI: 10.1007/s00414-010-0492-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 07/02/2010] [Indexed: 11/26/2022]
Abstract
This manuscript extends on earlier recommendations of the editor of the International Journal of Legal Medicine on short tandem repeat population data and provides details on specific criteria relevant for the analysis and publication of population studies on haploid DNA markers, i.e. Y-chromosomal polymorphisms and mitochondrial DNA. The proposed concept is based on review experience with the two forensic haploid markers databases YHRD and EMPOP, which are both endorsed by the International Society for Forensic Genetics. The intention is to provide guidance with the preparation of population studies and their results to improve the reviewing process and the quality of published data. We also suggest a minimal set of required information to be presented in the publication to increase understanding and use of the data. The outlined procedure has in part been elaborated with the editors of the journal Forensic Science International Genetics.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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Palencia L, Valverde L, Alvarez A, Cainé LM, Cardoso S, Alfonso-Sánchez MA, Pinheiro MF, de Pancorbo MM. Mitochondrial DNA diversity in a population from Santa Catarina (Brazil): predominance of the European input. Int J Legal Med 2010; 124:331-6. [PMID: 20480173 DOI: 10.1007/s00414-010-0464-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 04/29/2010] [Indexed: 12/16/2022]
Abstract
The state of Santa Catarina (Brazil) is known to have represented a cultural crossroads in South America due to several historic migrations mainly from Europe and Africa. We set out to scrutinize whether the genetic imprint of these migrations could be traced through analysis of the matrilineal gene pool of the Catarinenses. The entire control region of the mitochondrial DNA was studied in 80 healthy and maternally unrelated individuals. The analysis of haplogroup distribution revealed that this population is extremely heterogeneous, showing the coexistence of matrilineal lineages with three different phylogeographic origins. European lineages are the most frequent due mainly to the impact of relatively recent migratory waves from Europe. In spite of this, Native American lineages and African lineages incorporated with the slave trade are also present in noticeable proportions. The strikingly high variability generated by intense gene flow is mirrored in a high sequence diversity (0.9930) and power of discrimination (0.9806). Thus, analysis of the entire mitochondrial DNA control region emerges as a valuable tool for forensic genetic purposes in this highly admixed population, an attribute common to several present-day Latin American populations.
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Affiliation(s)
- Leire Palencia
- BIOMICs Research Group, Centro de Investigación y Estudios Avanzados Lucio Lascaray, Universidad del País Vasco UPV/EHU, Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
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Just RS, Loreille OM, Molto JE, Merriwether DA, Woodward SR, Matheson C, Creed J, McGrath SE, Sturk-Andreaggi K, Coble MD, Irwin JA, Ruffman A, Parr RL. Titanic's unknown child: the critical role of the mitochondrial DNA coding region in a re-identification effort. Forensic Sci Int Genet 2010; 5:231-5. [PMID: 20457081 DOI: 10.1016/j.fsigen.2010.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 01/04/2010] [Accepted: 01/20/2010] [Indexed: 11/19/2022]
Abstract
This report describes a re-examination of the remains of a young male child recovered in the Northwest Atlantic following the loss of the Royal Mail Ship Titanic in 1912 and buried as an unknown in Halifax, Nova Scotia shortly thereafter. Following exhumation of the grave in 2001, mitochondrial DNA (mtDNA) hypervariable region 1 sequencing and odontological examination of the extremely limited skeletal remains resulted in the identification of the child as Eino Viljami Panula, a 13-month-old Finnish boy. This paper details recent and more extensive mitochondrial genome analyses that indicate the remains are instead most likely those of an English child, Sidney Leslie Goodwin. The case demonstrates the benefit of targeted mtDNA coding region typing in difficult forensic cases, and highlights the need for entire mtDNA sequence databases appropriate for forensic use.
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Affiliation(s)
- Rebecca S Just
- Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, 1413 Research Blvd., Rockville, MD 20850, USA
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Molecular genetic identification of skeletal remains from the Second World War Konfin I mass grave in Slovenia. Int J Legal Med 2010; 124:307-17. [PMID: 20217112 PMCID: PMC2887502 DOI: 10.1007/s00414-010-0431-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 02/10/2010] [Indexed: 11/06/2022]
Abstract
This paper describes molecular genetic identification of one third of the skeletal remains of 88 victims of postwar (June 1945) killings found in the Konfin I mass grave in Slovenia. Living relatives were traced for 36 victims. We analyzed 84 right femurs and compared their genetic profiles to the genetic material of living relatives. We cleaned the bones, removed surface contamination, and ground the bones into powder. Prior to DNA isolation using Biorobot EZ1 (Qiagen), the powder was decalcified. The nuclear DNA of the samples was quantified using the real-time polymerase chain reaction method. We extracted 0.8 to 100 ng DNA/g of bone powder from 82 bones. Autosomal genetic profiles and Y-chromosome haplotypes were obtained from 98% of the bones, and mitochondrial DNA (mtDNA) haplotypes from 95% of the bones for the HVI region and from 98% of the bones for the HVII region. Genetic profiles of the nuclear and mtDNA were determined for reference persons. For traceability in the event of contamination, we created an elimination database including genetic profiles of the nuclear and mtDNA of all persons that had been in contact with the skeletal remains. When comparing genetic profiles, we matched 28 of the 84 bones analyzed with living relatives (brothers, sisters, sons, daughters, nephews, or cousins). The statistical analyses showed a high confidence of correct identification for all 28 victims in the Konfin I mass grave (posterior probability ranged from 99.9% to more than 99.999999%).
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Nilsson M, Possnert G, Edlund H, Budowle B, Kjellström A, Allen M. Analysis of the putative remains of a European patron saint--St. Birgitta. PLoS One 2010; 5:e8986. [PMID: 20169108 PMCID: PMC2821883 DOI: 10.1371/journal.pone.0008986] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 12/13/2009] [Indexed: 11/25/2022] Open
Abstract
Saint Birgitta (Saint Bridget of Sweden) lived between 1303 and 1373 and was designated one of Europe's six patron saints by the Pope in 1999. According to legend, the skulls of St. Birgitta and her daughter Katarina are maintained in a relic shrine in Vadstena abbey, mid Sweden. The origin of the two skulls was assessed first by analysis of mitochondrial DNA (mtDNA) to confirm a maternal relationship. The results of this analysis displayed several differences between the two individuals, thus supporting an interpretation of the two skulls not being individuals that are maternally related. Because the efficiency of PCR amplification and quantity of DNA suggested a different amount of degradation and possibly a very different age for each of the skulls, an orthogonal procedure, radiocarbon dating, was performed. The radiocarbon dating results suggest an age difference of at least 200 years and neither of the dating results coincides with the period St. Birgitta or her daughter Katarina lived. The relic, thought to originate from St. Birgitta, has an age corresponding to the 13th century (1215–1270 cal AD, 2σ confidence), which is older than expected. Thus, the two different analyses are consistent in questioning the authenticity of either of the human skulls maintained in the Vadstena relic shrine being that of St. Birgitta. Of course there are limitations when interpreting the data of any ancient biological materials and these must be considered for a final decision on the authenticity of the remains.
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Affiliation(s)
- Martina Nilsson
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Forensic Unit, Regional Criminal Investigation Department, Stockholm County Police, Stockholm, Sweden
| | - Göran Possnert
- The Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden
| | - Hanna Edlund
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Bruce Budowle
- FBI Laboratory, Quantico, Virginia, United States of America
- Department of Forensic and Investigative Genetics, University of North Texas Health Science Centre, Ft Worth, Texas, United States of America
| | - Anna Kjellström
- The Wallenberg Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Marie Allen
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
- * E-mail:
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El Ossmani H, Gazzaz B, El Harrak A, Boutayeb S, El Amri H. First identification of human remains using mtDNA sequence analysis in Genetic Laboratory of Royal Gendarmerie in Morocco. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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The impact of jumping alignments on mtDNA population analysis and database searching. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hall TA, Sannes-Lowery KA, McCurdy LD, Fisher C, Anderson T, Henthorne A, Gioeni L, Budowle B, Hofstadler SA. Base Composition Profiling of Human Mitochondrial DNA Using Polymerase Chain Reaction and Direct Automated Electrospray Ionization Mass Spectrometry. Anal Chem 2009; 81:7515-26. [DOI: 10.1021/ac901222y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Thomas A. Hall
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Kristin A. Sannes-Lowery
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Leslie D. McCurdy
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Constance Fisher
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Theodore Anderson
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Almira Henthorne
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Lora Gioeni
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Bruce Budowle
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Steven A. Hofstadler
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
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Pietrangeli I, Caruso V, Veneziano L, Spinella A, Arcudi G, Giardina E, Novelli G. Forensic DNA Challenges: Replacing Numbers with Names of Fosse Ardeatine’s Victims. J Forensic Sci 2009; 54:905-8. [DOI: 10.1111/j.1556-4029.2009.01052.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Just RS, Leney MD, Barritt SM, Los CW, Smith BC, Holland TD, Parsons TJ. The Use of Mitochondrial DNA Single Nucleotide Polymorphisms to Assist in the Resolution of Three Challenging Forensic Cases. J Forensic Sci 2009; 54:887-91. [DOI: 10.1111/j.1556-4029.2009.01069.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Turchi C, Buscemi L, Giacchino E, Onofri V, Fendt L, Parson W, Tagliabracci A. Polymorphisms of mtDNA control region in Tunisian and Moroccan populations: An enrichment of forensic mtDNA databases with Northern Africa data. Forensic Sci Int Genet 2009; 3:166-72. [DOI: 10.1016/j.fsigen.2009.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Stabilizing mtDNA sequence nomenclature with an operationally efficient approach. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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von Wurmb-Schwark N, Heinrich A, Freudenberg M, Gebühr M, Schwark T. The impact of DNA contamination of bone samples in forensic case analysis and anthropological research. Leg Med (Tokyo) 2008; 10:125-30. [DOI: 10.1016/j.legalmed.2007.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/10/2007] [Accepted: 10/03/2007] [Indexed: 10/22/2022]
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Evaluation of mitochondrial DNA coding region assays for increased discrimination in forensic analysis. Forensic Sci Int Genet 2008; 2:1-8. [DOI: 10.1016/j.fsigen.2007.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 07/09/2007] [Accepted: 07/18/2007] [Indexed: 11/15/2022]
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Zimmermann B, Brandstätter A, Duftner N, Niederwieser D, Spiroski M, Arsov T, Parson W. Mitochondrial DNA control region population data from Macedonia. Forensic Sci Int Genet 2007; 1:e4-9. [DOI: 10.1016/j.fsigen.2007.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 03/18/2007] [Indexed: 11/15/2022]
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Successful DNA typing of ultrafiltered urines used to detect EPO doping. Forensic Sci Int Genet 2007; 1:281-2. [DOI: 10.1016/j.fsigen.2007.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 02/19/2007] [Indexed: 11/22/2022]
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Turchi C, Buscemi L, Previderè C, Grignani P, Brandstätter A, Achilli A, Parson W, Tagliabracci A. Italian mitochondrial DNA database: results of a collaborative exercise and proficiency testing. Int J Legal Med 2007; 122:199-204. [PMID: 17952451 DOI: 10.1007/s00414-007-0207-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Accepted: 09/06/2007] [Indexed: 11/29/2022]
Abstract
This work is a review of a collaborative exercise on mtDNA analysis undertaken by the Italian working group (Ge.F.I.). A total of 593 samples from 11 forensic genetic laboratories were subjected to hypervariable region (HVS-I/HVS-II) sequence analysis. The raw lane data were sent to MtDNA Population Database (EMPOP) for an independent evaluation. For the inclusion of data for the Italian database, quality assurance procedures were applied to the control region profiles. Only eight laboratories with a final population sample of 395 subjects passed the quality conformance test. Control region haplogroup (hg) assignments were confirmed by restriction fragment length polymorphism (RFLP) typing of the most common European hg-diagnostic sites. A total of 306 unique haplotypes derived from the combined analysis of control and coding region polymorphisms were found; the most common haplotype--CRS, 263, 309.1C, 315.1C/ not7025 AluI--was shared by 20 subjects. The majority of mtDNAs detected in the Italian population fell into the most common west Eurasian hgs: R0a (0.76%), HV (4.81%), H (38.99%), HV0 (3.55%), J (7.85%), T (13.42%), U (11.65%), K (10.13%), I (1.52%), X (2.78%), and W (1.01%).
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Affiliation(s)
- Chiara Turchi
- Department of Neuroscience, Section of Legal Medicine, Università Politecnica delle Marche, 60020 Ancona, Italy
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