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Aquilano E, de la Fuente C, Rodríguez Golpe D, Motti JMB, Bravi CM. Sequencing errors in Native American mitogenomes: impact on clade definitions, haplogroup assignation, and beyond. Mitochondrion 2023; 70:54-58. [PMID: 37003527 DOI: 10.1016/j.mito.2023.03.005] [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: 09/06/2022] [Revised: 03/09/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
Available evidence allows the interpretation that some cases of absence of otherwise expected variation, based on phylogenetic expectations in mitogenomes of Native American origin, are due to artificial recombination rather than to homoplasy, while other more complex scenarios involving combination of original Cambridge Reference Sequence mistakes plus incomplete or incorrect scoring of variation are also showed. Several instances of mismatched control and coding regions as well as partially duplicated HV2 are observed in Peruvians, while intra-haplogroup chimaeras of different D1 subhaplogroups are referred to in Mexican Native Americans. A revised definition for haplogroup B2h is proposed, and preventive quality control measures are suggested.
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Affiliation(s)
- Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina
| | | | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina
| | - Josefina M B Motti
- Laboratorio de Ecología Evolutiva Humana (LEEH), Facultad de Ciencias Sociales (FACSO), Universidad Nacional del Centro de la Provincia de Buenos Aires-CONICET, Calle 508 #881, 7631 Quequén, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina.
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2
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Ta MTA, Nguyen NN, Tran DM, Nguyen TH, Vu TA, Le DT, Le PT, Do TTH, Hoang H, Chu HH. Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system. Int J Legal Med 2021; 135:2285-2294. [PMID: 34196785 DOI: 10.1007/s00414-021-02649-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
Mitochondrial DNA (mtDNA) analysis using Sanger sequencing has been a routine practice for the identification of human skeletal remains. However, this process is usually challenging since DNA from the remains is highly degraded and at low concentration. Recently, the advent and implementation of massively parallel sequencing (MPS) have been offered the ability to improve mtDNA sequence data for forensic analysis. To assess the utility of the Ion S5™ system - an MPS platform for mtDNA analysis in challenging samples, we sequenced the mitochondrial control region of 52 age-old skeletal remains. Using the Precision ID mtDNA Control Region Panel, 50 full and two partial control region haplotypes at relatively high mean coverage of 2494 × were achieved for variant calling. Further variant analysis at 10% threshold for point heteroplasmy showed high degradation degree in terms of DNA damage in our bone samples. A higher point heteroplasmy threshold of 20% was required to diminish most of background noise caused by the damage. The results from this study indicated the potential application of the Ion S5™ system in sequencing degraded samples in Vietnam and provided valuable data sources for forensic analyses in the future.
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Affiliation(s)
- May Thi Anh Ta
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nam Ngoc Nguyen
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Duc Minh Tran
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trang Hong Nguyen
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Tuan Anh Vu
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dung Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phuong Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thu Thi Hong Do
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Hoang Ha Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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3
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Bodner M, Parson W. The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets. Genes (Basel) 2020; 11:E901. [PMID: 32784546 PMCID: PMC7463946 DOI: 10.3390/genes11080901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 01/20/2023] Open
Abstract
STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates comprise additional STR loci and populations in the frequency database and many further STR-related aspects. One significant innovation is the autosomal STR data QC provided prior to publication of datasets. Such scrutiny was lacking previously, leaving QC to authors, reviewers and editors, which led to an unacceptably high error rate in scientific papers. The results from scrutinizing 184 STR datasets containing >177,000 individual genotypes submitted in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate. Almost no error-free submissions were received, which clearly shows that centralized QC and data curation are essential to maintain the high-quality standard required in forensic genetics. While many errors had minor impact on the resulting allele frequencies, multiple error categories were commonly found within single datasets. Several datasets contained serious flaws. We discuss the factors that caused the errors to draw the attention to redundant pitfalls and thus contribute to better quality of autosomal STR datasets and allele frequency reports.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA;
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Du HY, Zhang XY, Dinh TD, Ma Y, Zong C, Li GL, Dahmer TD, Xu YC. Identification of hybrid green peafowl using mitochondrial and nuclear markers. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01159-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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5
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Resolving mitochondrial haplogroups B2 and B4 with next-generation mitogenome sequencing to distinguish Native American from Asian haplotypes. Forensic Sci Int Genet 2019; 43:102143. [DOI: 10.1016/j.fsigen.2019.102143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
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6
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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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Bradbury C, Köttgen A, Staubach F. Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource. Forensic Sci Int Genet 2018; 38:93-104. [PMID: 30391626 DOI: 10.1016/j.fsigen.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 10/13/2018] [Indexed: 01/04/2023]
Abstract
With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application.
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Affiliation(s)
- Cedric Bradbury
- University College Freiburg, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Dept. of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Fabian Staubach
- Institute of Biology I, Dept. of Evolutionary Biology and Ecology, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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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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Palencia-Madrid L, Cardoso S, Castro-Maestre F, Baroja-Careaga I, Rocandio AM, de Pancorbo MM. Development of a new screening method to determine the main 52 mitochondrial haplogroups through a single minisequencing reaction. Mitochondrion 2018; 45:46-51. [PMID: 29474835 DOI: 10.1016/j.mito.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/23/2018] [Accepted: 02/15/2018] [Indexed: 12/17/2022]
Abstract
This work presents the design, development and optimization of a screening method based on single-base extension sequencing to simultaneously analyze a panel of 52 mitochondrial SNPs. This enables to recognize the main mitochondrial haplogroups and to discriminate even between lineages from the same phylogenetic branch that diverged in different continents. The unavailability of individuals harboring infrequent variants was a limitation to optimize the panel. To overcome this, we have modified DNA by site-directed mutagenesis to create the unavailable allelic variants. This allowed us to verify the reliability of this panel and its usefulness to be applied in biomedicine, forensic and population genetic studies.
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Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Sergio Cardoso
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Fernando Castro-Maestre
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Igor Baroja-Careaga
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Ana M Rocandio
- Department of Nutrition and Food Sciences, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.
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10
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Rakha A, Fatima, Peng MS, Adan A, Bi R, Yasmin M, Yao YG. mtDNA sequence diversity of Hazara ethnic group from Pakistan. Forensic Sci Int Genet 2017; 30:e1-e5. [DOI: 10.1016/j.fsigen.2017.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 07/02/2017] [Accepted: 07/08/2017] [Indexed: 10/19/2022]
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11
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Vanek D, Budowle B, Dubska-Votrubova J, Ambers A, Frolik J, Pospisek M, Al Afeefi AA, Al Hosani KI, Allen M, Al Naimi KS, Al Salafi D, Al Tayyari WAR, Arguetaa W, Bottinelli M, Bus MM, Cemper-Kiesslich J, Cepil O, De Cock G, Desmyter S, El Amri H, El Ossmani H, Galdies R, Grün S, Guidet F, Hoefges A, Iancu CB, Lotz P, Maresca A, Nagy M, Novotny J, Rachid H, Rothe J, Stenersen M, Stephenson M, Stevanovitch A, Strien J, Sumita DR, Vella J, Zander J. Results of a collaborative study on DNA identification of aged bone samples. Croat Med J 2017; 58:203-213. [PMID: 28613037 PMCID: PMC5470125 DOI: 10.3325/cmj.2017.58.203] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/31/2017] [Indexed: 11/10/2022] Open
Abstract
AIM A collaborative exercise with several institutes was organized by the Forensic DNA Service (FDNAS) and the Institute of the Legal Medicine, 2nd Faculty of Medicine, Charles University in Prague, Czech Republic, with the aim to test performance of different laboratories carrying out DNA analysis of relatively old bone samples. METHODS Eighteen laboratories participating in the collaborative exercise were asked to perform DNA typing of two samples of bone powder. Two bone samples provided by the National Museum and the Institute of Archaelogy in Prague, Czech Republic, came from archeological excavations and were estimated to be approximately 150 and 400 years old. The methods of genetic characterization including autosomal, gonosomal, and mitochondrial markers was selected solely at the discretion of the participating laboratory. RESULTS Although the participating laboratories used different extraction and amplification strategies, concordant results were obtained from the relatively intact 150 years old bone sample. Typing was more problematic with the analysis of the 400 years old bone sample due to poorer quality. CONCLUSION The laboratories performing identification DNA analysis of bone and teeth samples should regularly test their ability to correctly perform DNA-based identification on bone samples containing degraded DNA and potential inhibitors and demonstrate that risk of contamination is minimized.
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Affiliation(s)
- Daniel Vanek
- Daniel Vanek, Forensic DNA Service, Budinova 2, 180 81 Prague 8, Czech Republic,
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12
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Heinz T, Pala M, Gómez-Carballa A, Richards MB, Salas A. Updating the African human mitochondrial DNA tree: Relevance to forensic and population genetics. Forensic Sci Int Genet 2016; 27:156-159. [PMID: 28086175 DOI: 10.1016/j.fsigen.2016.12.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/14/2016] [Accepted: 12/30/2016] [Indexed: 11/24/2022]
Abstract
Analysis of human mitochondrial DNA (mtDNA) variation plays an important role in forensic genetic investigations, especially in degraded biological samples and hair shafts. There are many issues of the mtDNA phylogeny that are of special interest to the forensic community, such as haplogroup classification or the post hoc investigation of potential errors in mtDNA datasets. We have analyzed >2200 mitogenomes of African ancestry with the aim of improving the known worldwide phylogeny. More than 300 new minor subclades were identified, and the Time to the Most Recent Common Ancestor (TMRCA) was estimated for each node of the phylogeny. Phylogeographic details are provided which might also be relevant to forensic genetics. The present study has special interest for forensic investigations because current analysis and interpretation of mtDNA casework rest on a solid worldwide phylogeny, as is evident from the role that phylogeny plays in popular resources in the field (e.g. PhyloTree), software (e.g. Haplogrep 2), and databases (e.g. EMPOP). Apart from this forensic genetic interest, we also highlight the impact of this research in anthropological studies, such as those related to the reconstruction of the transatlantic slave trade.
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Affiliation(s)
- Tanja Heinz
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.
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Bodner M, Bastisch I, Butler JM, Fimmers R, Gill P, Gusmão L, Morling N, Phillips C, Prinz M, Schneider PM, Parson W. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER). Forensic Sci Int Genet 2016; 24:97-102. [DOI: 10.1016/j.fsigen.2016.06.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 06/11/2016] [Indexed: 01/20/2023]
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14
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Hairy matters: MtDNA quantity and sequence variation along and among human head hairs. Forensic Sci Int Genet 2016; 25:1-9. [PMID: 27484846 DOI: 10.1016/j.fsigen.2016.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/20/2016] [Accepted: 07/23/2016] [Indexed: 01/31/2023]
Abstract
Hairs from the same donor have been found to differ in mtDNA sequence within and among themselves and from other tissues, which impacts interpretation of results obtained in a forensic setting. However, little is known on the magnitude of this phenomenon and published data on systematic studies are scarce. We addressed this issue by generating mtDNA control region (CR) profiles of >450 hair fragments from 21 donors by Sanger-type sequencing (STS). To mirror forensic scenarios, we compared hair haplotypes from the same donors to each other, to the corresponding buccal swab reference haplotypes and analyzed several fragments of individual hairs. We also investigated the effects of hair color, donor sex and age, mtDNA haplogroup and chemical treatment on mtDNA quantity, amplification success and variation. We observed a wide range of individual CR sequence variation. The reference haplotype was the only or most common (≥75%) hair haplotype for most donors. However, in two individuals, the reference haplotype was only found in about a third of the investigated hairs, mainly due to differences at highly variable positions. Similarly, most hairs revealed the reference haplotype along their entire length, however, about a fifth of the hairs contained up to 71% of segments with deviant haplotypes, independent of the longitudinal position. Variation affected numerous positions, typically restricted to the individual hair and in most cases heteroplasmic, but also fixed (i.e. homoplasmic) substitutions were observed. While existing forensic mtDNA interpretation guidelines were found still sufficient for all comparisons to reference haplotypes, some comparisons between hairs from the same donor could yield false exclusions when those guidelines are strictly followed. This study pinpoints the special care required when interpreting mtDNA results from hair in forensic casework.
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15
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Børsting C, Morling N. Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 2015; 18:78-89. [DOI: 10.1016/j.fsigen.2015.02.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/12/2015] [Accepted: 02/11/2015] [Indexed: 12/13/2022]
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16
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DNA Commission of the International Society for Forensic Genetics: Revised and extended guidelines for mitochondrial DNA typing. Forensic Sci Int Genet 2014; 13:134-42. [DOI: 10.1016/j.fsigen.2014.07.010] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 07/19/2014] [Indexed: 11/21/2022]
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17
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King JL, Sajantila A, Budowle B. mitoSAVE: mitochondrial sequence analysis of variants in Excel. Forensic Sci Int Genet 2014; 12:122-5. [PMID: 24952129 DOI: 10.1016/j.fsigen.2014.05.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 05/20/2014] [Accepted: 05/26/2014] [Indexed: 12/21/2022]
Abstract
The mitochondrial genome (mtGenome) contains genetic information amenable to numerous applications such as medical research, population and evolutionary studies, and human identity testing. However, inconsistent nomenclature assignment makes haplotype comparison difficult and can lead to false exclusion of potentially useful profiles. Massively Parallel Sequencing (MPS) is a platform for sequencing large datasets and potentially whole populations with relative ease. However, the data generated are not easily parsed and interpreted. With this in mind, mitoSAVE has been developed to enable fast conversion of Variant Call Format (VCF) files. mitoSAVE is an Excel-based workbook that converts data within the VCF into mtDNA haplotypes using phylogenetically-established nomenclature as well as rule-based alignments consistent with current forensic standards. mitoSAVE is formatted for human mitochondrial genome; however, it can easily be adapted to support other reasonably small genomes.
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Affiliation(s)
- Jonathan L King
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA.
| | - Antti Sajantila
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA; Department of Forensic Medicine, Hjelt Institute, P.O. Box 40, 00014 University of Helsinki, Helsinki, Finland
| | - Bruce Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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18
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Angleby H, Oskarsson M, Pang J, Zhang YP, Leitner T, Braham C, Arvestad L, Lundeberg J, Webb KM, Savolainen P. Forensic informativity of ~3000 bp of coding sequence of domestic dog mtDNA. J Forensic Sci 2014; 59:898-908. [PMID: 24814664 DOI: 10.1111/1556-4029.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 05/10/2013] [Indexed: 11/30/2022]
Abstract
The discriminatory power of the noncoding control region (CR) of domestic dog mitochondrial DNA alone is relatively low. The extent to which the discriminatory power could be increased by analyzing additional highly variable coding regions of the mitochondrial genome (mtGenome) was therefore investigated. Genetic variability across the mtGenome was evaluated by phylogenetic analysis, and the three most variable ~1 kb coding regions identified. We then sampled 100 Swedish dogs to represent breeds in accordance with their frequency in the Swedish population. A previously published dataset of 59 dog mtGenomes collected in the United States was also analyzed. Inclusion of the three coding regions increased the exclusion capacity considerably for the Swedish sample, from 0.920 for the CR alone to 0.964 for all four regions. The number of mtDNA types among all 159 dogs increased from 41 to 72, the four most frequent CR haplotypes being resolved into 22 different haplotypes.
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Affiliation(s)
- Helen Angleby
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, School of Biotechnology, SE-171 65, Solna, Sweden
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Verscheure S, Backeljau T, Desmyter S. Reviewing population studies for forensic purposes: Dog mitochondrial DNA. Zookeys 2013:381-411. [PMID: 24453568 PMCID: PMC3890688 DOI: 10.3897/zookeys.365.5859] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 12/14/2013] [Indexed: 02/02/2023] Open
Abstract
The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework.
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Affiliation(s)
- Sophie Verscheure
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium ; University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020, Antwerp, Belgium
| | - Thierry Backeljau
- University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020, Antwerp, Belgium ; Royal Belgian Institute of Natural Sciences (OD "Taxonomy and Phylogeny" and JEMU), Vautierstraat 29, B-1000, Brussels, Belgium
| | - Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
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Mass spectrometric base composition profiling: Implications for forensic mtDNA databasing. Forensic Sci Int Genet 2013; 7:587-592. [PMID: 24054029 PMCID: PMC3820008 DOI: 10.1016/j.fsigen.2013.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/09/2013] [Accepted: 05/19/2013] [Indexed: 11/24/2022]
Abstract
In forensic genetics mitochondrial DNA (mtDNA) is usually analyzed by direct Sanger-type sequencing (STS). This method is known to be laborious and sometimes prone to human error. Alternative methods have been proposed that lead to faster results. Among these are methods that involve mass-spectrometry resulting in base composition profiles that are, by definition, less informative than the full nucleotide sequence. Here, we applied a highly automated electrospray ionization mass spectrometry (ESI-MS) system (PLEX-ID) to an mtDNA population study to compare its performance with respect to throughput and concordance to STS. We found that the loss of information power was relatively low compared to the gain in speed and analytical standardization. The detection of point and length heteroplasmy turned out to be roughly comparable between the technologies with some individual differences related to the processes. We confirm that ESI-MS provides a valuable platform for analyzing mtDNA variation that can also be applied in the forensic context.
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Prieto L, Alves C, Zimmermann B, Tagliabracci A, Prieto V, Montesino M, Whittle M, Anjos M, Cardoso S, Heinrichs B, Hernandez A, López-Parra A, Sala A, Saragoni V, Burgos G, Marino M, Paredes M, Mora-Torres C, Angulo R, Chemale G, Vullo C, Sánchez-Simón M, Comas D, Puente J, López-Cubría C, Modesti N, Aler M, Merigioli S, Betancor E, Pedrosa S, Plaza G, Masciovecchio M, Schneider P, Parson W. GHEP-ISFG proficiency test 2011: Paper challenge on evaluation of mitochondrial DNA results. Forensic Sci Int Genet 2013; 7:10-5. [DOI: 10.1016/j.fsigen.2012.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 04/06/2012] [Accepted: 04/20/2012] [Indexed: 11/16/2022]
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Melton T, Dimick G, Higgins B, Yon M, Holland C. Mitochondrial DNA analysis of 114 hairs measuring less than 1 cm from a 19-year-old homicide. INVESTIGATIVE GENETICS 2012; 3:12. [PMID: 22686607 PMCID: PMC3398847 DOI: 10.1186/2041-2223-3-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 06/11/2012] [Indexed: 11/18/2022]
Abstract
Background Mitochondrial DNA analysis is typically applied to degraded skeletal remains and telogen or rootless hairs. Data on the application of the method to very small hairs less than 0.5 cm from an age-matched and -challenged sample set are lacking. Methods One hundred fourteen hairs sized less than 1 cm from a 1993 case were analyzed for mitochondrial DNA according to laboratory standard operating procedures. For some hairs, a screening approach was applied, which permitted some samples, such as victim hairs on victim clothing, to be eliminated from the process quickly. Degraded samples were amplified with “mini-primers,” and 12S species testing was applied when non-human hairs were encountered. Results Partial to full control region human mitochondrial DNA profiles or species identifications (non-human species) were obtained from 93% of hairs under 1 cm, 92% of hairs under 5 mm, and 90% of hairs under 3.5 mm. Nineteen of 21 hairs 2 mm or less gave full or partial profiles. Among 128 hairs of all sizes tested in the case, 9 gave no results, 3 were canine in origin, and 73 did not exclude six known individuals tested in the case. Twenty-two hairs had nine additional profiles that were observed two or more times each. Twenty-one hairs showed singleton types not matching each other or any individual. Conclusions Crime scene hairs that are both aged and small are often judged to be unsuitable for either hair microscopy or DNA analysis. This study of age-matched challenged small hairs indicates that even the smallest probative crime scene hairs are suitable for mitochondrial DNA analysis and can provide useful data.
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Affiliation(s)
- Terry Melton
- Mitotyping Technologies, 2565 Park Center Boulevard, Suite 200, State College, PA, USA.
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23
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Milia N, Congiu A, Anagnostou P, Montinaro F, Capocasa M, Sanna E, Destro Bisol G. Mine, yours, ours? Sharing data on human genetic variation. PLoS One 2012; 7:e37552. [PMID: 22679483 PMCID: PMC3367958 DOI: 10.1371/journal.pone.0037552] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 04/25/2012] [Indexed: 11/29/2022] Open
Abstract
The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. Empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establishment of widespread sharing of primary datasets. However, no specific analysis has been conducted to date in order to ascertain whether the sharing of primary datasets is common-practice in this research field. To this aim, we analyzed a total of 543 mitochondrial and Y chromosomal datasets reported in 508 papers indexed in the Pubmed database from 2008 to 2011. A substantial portion of datasets (21.9%) was found to have been withheld, while neither strong editorial policies nor high impact factor proved to be effective in increasing the sharing rate beyond the current figure of 80.5%. Disaggregating datasets for research fields, we could observe a substantially lower sharing in medical than evolutionary and forensic genetics, more evident for whole mtDNA sequences (15.0% vs 99.6%). The low rate of positive responses to e-mail requests sent to corresponding authors of withheld datasets (28.6%) suggests that sharing should be regarded as a prerequisite for final paper acceptance, while making authors deposit their results in open online databases which provide data quality control seems to provide the best-practice standard. Finally, we estimated that 29.8% to 32.9% of total resources are used to generate withheld datasets, implying that an important portion of research funding does not produce shared knowledge. By making the scientific community and the public aware of this important aspect, we may help popularize a more effective culture of data sharing.
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Affiliation(s)
- Nicola Milia
- Dipartimento di Biologia Ambientale, Università di Roma La Sapienza, Roma Italy
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Núnéz C, Sosa C, Baeta M, Geppert M, Turnbough M, Phillips N, Casalod Y, Bolea M, Roby R, Budowle B, Martínez-Jarreta B. Genetic analysis of 7 medieval skeletons from the Aragonese Pyrenees. Croat Med J 2012; 52:336-43. [PMID: 21674829 PMCID: PMC3118721 DOI: 10.3325/cmj.2011.52.336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aim To perform a genetic characterization of 7 skeletons from medieval age found in a burial site in the Aragonese Pyrenees. Methods Allele frequencies of autosomal short tandem repeats (STR) loci were determined by 3 different STR systems. Mitochondrial DNA (mtDNA) and Y-chromosome haplogroups were determined by sequencing of the hypervariable segment 1 of mtDNA and typing of phylogenetic Y chromosome single nucleotide polymorphisms (Y-SNP) markers, respectively. Possible familial relationships were also investigated. Results Complete or partial STR profiles were obtained in 3 of the 7 samples. Mitochondrial DNA haplogroup was determined in 6 samples, with 5 of them corresponding to the haplogroup H and 1 to the haplogroup U5a. Y-chromosome haplogroup was determined in 2 samples, corresponding to the haplogroup R. In one of them, the sub-branch R1b1b2 was determined. mtDNA sequences indicated that some of the individuals could be maternally related, while STR profiles indicated no direct family relationships. Conclusions Despite the antiquity of the samples and great difficulty that genetic analyses entail, the combined use of autosomal STR markers, Y-chromosome informative SNPs, and mtDNA sequences allowed us to genotype a group of skeletons from the medieval age.
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Affiliation(s)
- Carolina Núnéz
- Department of Forensic Medicine, Faculty of Medicine, University of Zaragoza, Zaragoza, Spain.
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Grzybowski T, Rogalla U. Mitochondria in anthropology and forensic medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 942:441-53. [PMID: 22399435 DOI: 10.1007/978-94-007-2869-1_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Mitochondria's role in crucial metabolic pathways is probably the first answer which comes to our minds for the question: what do these tiny organelles serve for? However, specific features of their DNA made them extremely useful also in the field of anthropology and forensics. MtDNA analyses became a milestone in the complex task of unraveling earliest human migrations. Evidence provided by these experiments left no doubts on modern humans origins pointing to Africa being our cradle. It also contributed to interpretation of putative ways of our dispersal around Asia and Americas thousands years ago. On the other hand, analysis of mtDNA is well established and valuable tool in forensic genetics. When other definitely more popular markers give no answer on identity, it is the time to employ information carried by mitochondria. This chapter summarizes not only current reports on the role of mitochondria in forensics and reconstruction of modern humans phylogeny, but also calls one's attention to a broad range of difficulties and constraints associated with mtDNA analyses.
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Affiliation(s)
- Tomasz Grzybowski
- Department of Molecular and Forensic Genetics, The Nicolaus Copernicus University, Bydgoszcz, Poland.
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Current genetic methodologies in the identification of disaster victims and in forensic analysis. J Appl Genet 2011; 53:41-60. [PMID: 22002120 PMCID: PMC3265735 DOI: 10.1007/s13353-011-0068-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 12/16/2022]
Abstract
This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures).
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Repiská V, Lehocky’ I, Galatová J, Böhmer D. Haplotypes of mtDNA-HV1/HV2 in non-related individuals of caucasian population living in the Slovak Republic. Mol Biol 2010. [DOI: 10.1134/s0026893310060038] [Citation(s) in RCA: 2] [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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Prieto L, Zimmermann B, Goios A, Rodriguez-Monge A, Paneto GG, Alves C, Alonso A, Fridman C, Cardoso S, Lima G, Anjos MJ, Whittle MR, Montesino M, Cicarelli RMB, Rocha AM, Albarrán C, de Pancorbo MM, Pinheiro MF, Carvalho M, Sumita DR, Parson W. The GHEP-EMPOP collaboration on mtDNA population data--A new resource for forensic casework. Forensic Sci Int Genet 2010; 5:146-51. [PMID: 21075696 PMCID: PMC3065011 DOI: 10.1016/j.fsigen.2010.10.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP–EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org).
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Affiliation(s)
- L Prieto
- Comisaría General de Policía Científica, University Institute of Research in Forensic Sciences (IUICP), Madrid, Spain
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Brück S, Evers H, Heidorn F, Müller U, Kilper R, Verhoff MA. Single Cells for Forensic DNA Analysis-From Evidence Material to Test Tube. J Forensic Sci 2010; 56:176-80. [DOI: 10.1111/j.1556-4029.2010.01553.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [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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Grignani P, Turchi C, Achilli A, Peloso G, Alù M, Ricci U, Robino C, Pelotti S, Carnevali E, Boschi I, Tagliabracci A, Previderè C. Multiplex mtDNA coding region SNP assays for molecular dissection of haplogroups U/K and J/T. Forensic Sci Int Genet 2009; 4:21-5. [DOI: 10.1016/j.fsigen.2009.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 03/23/2009] [Accepted: 04/02/2009] [Indexed: 11/28/2022]
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Fendt L, Zimmermann B, Daniaux M, Parson W. Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences. BMC Genomics 2009; 10:139. [PMID: 19331681 PMCID: PMC2669098 DOI: 10.1186/1471-2164-10-139] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 03/30/2009] [Indexed: 11/18/2022] Open
Abstract
Background It has been demonstrated that a reliable and fail-safe sequencing strategy is mandatory for high-quality analysis of mitochondrial (mt) DNA, as the sequencing and base-calling process is prone to error. Here, we present a high quality, reliable and easy handling manual procedure for the sequencing of full mt genomes that is also appropriate for laboratories where fully automated processes are not available. Results We amplified whole mitochondrial genomes as two overlapping PCR-fragments comprising each about 8500 bases in length. We developed a set of 96 primers that can be applied to a (manual) 96 well-based technology, which resulted in at least double strand sequence coverage of the entire coding region (codR). Conclusion This elaborated sequencing strategy is straightforward and allows for an unambiguous sequence analysis and interpretation including sometimes challenging phenomena such as point and length heteroplasmy that are relevant for the investigation of forensic and clinical samples.
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Affiliation(s)
- Liane Fendt
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, Austria.
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Amorim A. A cautionary note on the evaluation of genetic evidence from uniparentally transmitted markers. Forensic Sci Int Genet 2008; 2:376-8. [PMID: 19083851 DOI: 10.1016/j.fsigen.2008.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/30/2008] [Accepted: 04/01/2008] [Indexed: 10/22/2022]
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The SNPforID browser: an online tool for query and display of frequency data from the SNPforID project. Int J Legal Med 2008; 122:435-40. [DOI: 10.1007/s00414-008-0233-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 03/13/2008] [Indexed: 11/26/2022]
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Brandstätter A, Egyed B, Zimmermann B, Tordai A, Padar Z, Parson W. Mitochondrial DNA control region variation in Ashkenazi Jews from Hungary. Forensic Sci Int Genet 2008; 2:e4-6. [DOI: 10.1016/j.fsigen.2007.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 07/25/2007] [Indexed: 10/22/2022]
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Parson W, Fendt L, Ballard D, Børsting C, Brinkmann B, Carracedo Á, Carvalho M, Coble MD, Real FC, Desmyter S, Dupuy BM, Harrison C, Hohoff C, Just R, Krämer T, Morling N, Salas A, Schmitter H, Schneider PM, Sonntag ML, Vallone PM, Brandstätter A. Identification of West Eurasian mitochondrial haplogroups by mtDNA SNP screening: Results of the 2006–2007 EDNAP collaborative exercise. Forensic Sci Int Genet 2008; 2:61-8. [DOI: 10.1016/j.fsigen.2007.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2007] [Accepted: 08/13/2007] [Indexed: 11/15/2022]
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Alshamali F, Brandstätter A, Zimmermann B, Parson W. Mitochondrial DNA control region variation in Dubai, United Arab Emirates. Forensic Sci Int Genet 2008; 2:e9-10. [DOI: 10.1016/j.fsigen.2007.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 08/08/2007] [Accepted: 08/09/2007] [Indexed: 10/22/2022]
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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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ISFG: Recommendations on biostatistics in paternity testing. Forensic Sci Int Genet 2007; 1:223-31. [DOI: 10.1016/j.fsigen.2007.06.006] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2007] [Accepted: 06/27/2007] [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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Lutz-Bonengel S, Sänger T, Parson W, Müller H, Ellwart JW, Follo M, Bonengel B, Niederstätter H, Heinrich M, Schmidt U. Single lymphocytes from two healthy individuals with mitochondrial point heteroplasmy are mainly homoplasmic. Int J Legal Med 2007; 122:189-97. [PMID: 17922134 DOI: 10.1007/s00414-007-0190-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 07/26/2007] [Indexed: 11/26/2022]
Abstract
The nature of mitochondrial DNA heteroplasmy is still unclear. It could either be caused by two mitochondrial DNA (mtDNA) haplotypes coexisting within a single cell or by an admixture of homoplasmic cells, each of which contains only one type of mtDNA molecule. To address this question, single lymphocytes were separated by flow cytometry assisted cell sorting and analyzed by cycle sequencing or minisequencing. To attain the required PCR sensitivity, the reactions were carried out on the surface of chemically structured glass slides in a reaction volume of 1-2 microl. In this study, blood samples from two healthy donors showing mitochondrial point heteroplasmy in direct sequencing (195Y and 234R, respectively) were analyzed. Nearly 96% of single lymphocytes tested were found to be in a homoplasmic state, but heteroplasmic cells were also detected. These results suggest that mitochondrial point heteroplasmy in blood may well be mainly due to the mixture of homoplasmic cells.
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Affiliation(s)
- Sabine Lutz-Bonengel
- Institute of Legal Medicine, Albert Ludwig University Freiburg, Albertstrasse 9, 79104 Freiburg, Germany.
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Parson W, Dür A. EMPOP--a forensic mtDNA database. Forensic Sci Int Genet 2007; 1:88-92. [PMID: 19083735 DOI: 10.1016/j.fsigen.2007.01.018] [Citation(s) in RCA: 257] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 01/27/2007] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA databases stand as the basis for frequency estimations of mtDNA sequences that became relevant in a case. The establishment of mtDNA databases sounds trivial; however, it has been shown in the past that this undertaking is prone to error for several reasons, particularly human error. We have established a concept for mtDNA data generation, analysis, transfer and quality control that meets forensic standards. Due to the complexity of mtDNA population data tables it is often difficult if not impossible to detect errors, especially for the untrained eye. We developed software based on quasi-median network analysis that visualizes mtDNA data tables and thus signposts sequencing, interpretation and transcription errors. The mtDNA data (N=5173; release 1) are stored and made publicly available via the Internet in the form of the EDNAP mtDNA Population Database, short EMPOP. This website also facilitates quasi-median network analysis and provides results that can be used to check the quality of mtDNA sequence data. EMPOP has been launched on 16 October 2006 and is since then available at http://www.empop.org.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University Müllerstreet 44, 6020 Innsbruck, Austria.
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Finnish mitochondrial DNA HVS-I and HVS-II population data. Forensic Sci Int 2007; 172:171-8. [PMID: 17336475 DOI: 10.1016/j.forsciint.2006.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 09/26/2006] [Accepted: 09/26/2006] [Indexed: 11/16/2022]
Abstract
We have analyzed the two hypervariable regions HVS-I and HVS-II of 200 Finnish male individuals for forensic purposes. The distribution of the haplotypes within Finland was determined by the geographical knowledge of the donors' maternal ancestors. In our population sample, we identified 135 different mtDNA haplotypes. Different mtDNA sequences were further divided to haplogroups using the EMPOP software. The most common haplogroups were H (40.0%) and U (27.5%). Subgroup U5b, which contains earlier described "Saami motif", consisted majority (65.5%) of the sample in the U haplogroup. Analysis of the mtDNA sequence hypervariable regions I and II showed that the mtDNA diversity within the Finnish population sample was comparable to other European populations and uniformly distributed. This is contrary to the Y-STR "minimal haplotype" diversity, which in Finland is lower than in any of the other European populations studied so far.
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Schneider PM. Scientific standards for studies in forensic genetics. Forensic Sci Int 2007; 165:238-43. [PMID: 16875790 DOI: 10.1016/j.forsciint.2006.06.067] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 06/13/2006] [Accepted: 06/19/2006] [Indexed: 11/16/2022]
Abstract
Forensic molecular genetics has evolved from a rapidly developing field with changing technologies into a highly recognized and generally accepted forensic science, leading to the establishment of national DNA databases with DNA profiles from suspects and convicted offenders. DNA evidence has taken a central role by carrying a significant weight for convictions, as well as by excluding innocent suspects early on in a criminal investigation. Due to this impact on the criminal justice system, guidelines for research in forensic genetics have been introduced already since many years. The most important issues regarding the selection and definition of typing systems both for paternity testing and for forensic identification, the criteria for technical and biostatistical validation, as well as the use of mitochondrial DNA analysis are summarized and discussed.
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Affiliation(s)
- Peter M Schneider
- Institute of Legal Medicine, University of Cologne, Melatenguertel 60-62, D-50858 Cologne, Germany.
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Parson W, Bandelt HJ. Extended guidelines for mtDNA typing of population data in forensic science. Forensic Sci Int Genet 2006; 1:13-9. [PMID: 19083723 DOI: 10.1016/j.fsigen.2006.11.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 11/16/2006] [Accepted: 11/19/2006] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA analysis has become a vital niche in forensic science as it constitutes a powerful technique for low quality and low quantity DNA samples. For the forensic field it is important to employ standardized procedures based on scientific grounds, in order to have mtDNA evidence be accepted in court. Here, we modify and extend recommendations that were spelled out previously in the absence of solid knowledge about the worldwide phylogeny. Refinement of those earlier guidelines became necessary in regard to sample selection, amplification and sequencing strategies, as well as a posteriori quality control of mtDNA profiles. The notation of sequence data should thus reflect this growing knowledge.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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Mathet VL, Cuestas ML, Ruiz V, Minassian ML, Rivero C, Trinks J, Daleoso G, León LM, Sala A, Libellara B, Corach D, Oubiña JR. Detection of hepatitis B virus (HBV) genotype E carried--even in the presence of high titers of anti-HBs antibodies--by an Argentinean patient of African descent who had received vaccination against HBV. J Clin Microbiol 2006; 44:3435-9. [PMID: 16954295 PMCID: PMC1594728 DOI: 10.1128/jcm.00866-06] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genotype E hepatitis B virus (HBV) was detected in two Argentine sisters exhibiting an African mitochondrial lineage. One of them (who had been vaccinated against HBV) exhibited anti-HBs cocirculating antibodies without HBsAg escape mutants, while her unvaccinated sister showed a D144A HBsAg escape mutant without anti-HBs antibodies. Both sisters carried an unusual L209V substitution within HBsAg.
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Affiliation(s)
- Verónica L Mathet
- Departamento Microbiología, Centro para el Estudio de Hepatitis Virales, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 11, 1121 Buenos Aires, Argentina
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Brandstätter A, Klein R, Duftner N, Wiegand P, Parson W. Application of a quasi-median network analysis for the visualization of character conflicts to a population sample of mitochondrial DNA control region sequences from southern Germany (Ulm). Int J Legal Med 2006; 120:310-4. [PMID: 16871406 DOI: 10.1007/s00414-006-0114-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 06/12/2006] [Indexed: 11/28/2022]
Abstract
Entire mtDNA control region sequences from 100 individuals in a west Eurasian population sample from southern Germany (around the city of Ulm) were generated and analyzed. The control region was amplified in one piece and sequenced with ten different sequencing primers. Sequence evaluation was performed independently. Phylogenetic analyses were used for quality assurance purposes and for the determination of the haplogroup affiliation of the samples. The sequences were scrutinized performing a quasi-median network analysis. To visualize character conflicts, frequent mutations were filtered, and the reduced data were represented by the torso of their quasi-median network. Character incompatibilities were found to be based on real biological patterns of homoplasy. The population data will be incorporated in the EMPOP database ( http://www.empop.org ).
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Affiliation(s)
- Anita Brandstätter
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, Innsbruck, 6020, Austria
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Brandstätter A, Niederstätter H, Pavlic M, Grubwieser P, Parson W. Generating population data for the EMPOP database - an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example. Forensic Sci Int 2006; 166:164-75. [PMID: 16829006 DOI: 10.1016/j.forsciint.2006.05.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 05/09/2006] [Accepted: 05/09/2006] [Indexed: 11/27/2022]
Abstract
The European DNA profiling group (EDNAP) mtDNA population database (EMPOP) is an international collaborative project between DNA laboratories performing mtDNA analysis and the DNA laboratory of the Institute of Legal Medicine (GMI) in Innsbruck, Austria. The goal is to set up a directly accessible mtDNA population database, which can be used in routine forensic casework for frequency investigations. Here we describe a safe laboratory scheme involving electronical data handling and computer-aided data transfer, which help to minimize errors originating from potential sample mix-up, data misinterpretation and incorrect transcription. The procedure is demonstrated by example of an mtDNA control region population study on 273 unrelated individuals from Austria. Our population sample was compared with five other European populations via an analysis of molecular variance (AMOVA). The inclusion of regions outside HVS-I and HVS-II increased the amount of information on the haplogroup diagnostic sites in the control region. Most of the haplotypes in Austrians fell into haplogroups H, J, K, T, and U. The random match probability in Austrians was 1:125; the average number of nucleotide differences between individuals in the Austrian database was 9.32.
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Affiliation(s)
- Anita Brandstätter
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstr. 44, 6020 Innsbruck, Austria
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