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Damaso N, Elwick KE, Robertson JM. Guidelines for the Analysis of DNA Barcoding/Metabarcoding Sequencing Data and Interpretation of Publicly Available Databases. Methods Mol Biol 2024; 2744:391-402. [PMID: 38683333 DOI: 10.1007/978-1-0716-3581-0_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
This chapter describes procedures for the use of DNA sequence data to obtain and compare taxonomic identification using the public databases GenBank and Barcode of Life Data System (BOLD). The chapter begins by describing procedures used to prepare quality sequences for uploading into GenBank and BOLD. Next, steps used to query the DNA sequences against the public databases are described using GenBank BLAST and BOLD identification engines. Interpretation guidelines for the taxonomic identification assignments are presented. Finally, a procedure for evaluating the accuracy and reliability of sequences from GenBank and BOLD is provided.
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Affiliation(s)
- Natalie Damaso
- Counter WMD Systems, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, MA, USA
| | - Kyleen E Elwick
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA, USA
| | - James M Robertson
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA, USA.
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2
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Elwick KE, Damaso N, Robertson JM. DNA Barcoding and Metabarcoding Protocols for Species Identification. Methods Mol Biol 2024; 2744:155-169. [PMID: 38683317 DOI: 10.1007/978-1-0716-3581-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.
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Affiliation(s)
- Kyleen E Elwick
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA, USA
| | - Natalie Damaso
- Counter WMD Systems, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, MA, USA
| | - James M Robertson
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA, USA.
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3
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Streicher MB, Johnson SD, Willows‐Munro S. Effect of fuchsin fixation of pollen on DNA barcode recovery. Ecol Evol 2023; 13:e10475. [PMID: 37664513 PMCID: PMC10468989 DOI: 10.1002/ece3.10475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 09/05/2023] Open
Abstract
Pollen grains attached to insects are a valuable source of ecological information which can be used to reconstruct visitation networks. Morphological pollen identification relies on light microscopy with pollen usually stained and mounted in fuchsin jelly, which is also used to remove pollen from the bodies of insects. Pollen embedded in fuchsin jelly could potentially be used for DNA barcoding and metabarcoding (large-scale taxonomic identification of complex mixed samples) and thus provide additional information for pollination networks. In this study, we determine whether fuchsin-embedded pollen can be used for downstream molecular applications. We evaluate the quality of plant barcode (ITS) sequences amplified from DNA extracted from both fresh (untreated) pollen, and pollen which had been embedded in fuchsin jelly. We show that the addition of fuchsin to DNA extraction does not impact DNA barcode sequence quality during short-term storage. DNA extractions from both untreated and fuchsin-treated pollen produced reliable barcode sequences of high quality. Our findings suggest that pollen which has been collected, stained, and embedded in fuchsin jelly for preliminary microscopy work can be used within several days for downstream genetic analysis, though the quality of DNA from pollen stored in fuchsin jelly for extended periods is yet to be established.
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Affiliation(s)
- Melanie B. Streicher
- Centre for Functional Biodiversity, School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
| | - Steven D. Johnson
- Centre for Functional Biodiversity, School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
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4
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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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5
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Phillips JD, Athey TB, McNicholas PD, Hanner RH. VLF: An R package for the analysis of very low frequency variants in DNA sequences. Biodivers Data J 2023; 11:e96480. [PMID: 38327328 PMCID: PMC10848336 DOI: 10.3897/bdj.11.e96480] [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: 10/18/2022] [Accepted: 11/30/2022] [Indexed: 01/27/2023] Open
Abstract
Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer Science and Department of Integrative Biology, University of Guelph, Guelph, CanadaSchool of Computer Science and Department of Integrative Biology, University of GuelphGuelphCanada
| | - Taryn B.T. Athey
- Stollery Children's Hospital, Edmonton, CanadaStollery Children's HospitalEdmontonCanada
| | - Paul D. McNicholas
- Department of Mathematics and Statistics, McMaster University, Hamilton, CanadaDepartment of Mathematics and Statistics, McMaster UniversityHamiltonCanada
| | - Robert H. Hanner
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, CanadaBiodiversity Institute of Ontario and Department of Integrative Biology, University of GuelphGuelphCanada
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6
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Sturk-Andreaggi K, Ring JD, Ameur A, Gyllensten U, Bodner M, Parson W, Marshall C, Allen M. The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes. Int J Mol Sci 2022; 23:ijms23042244. [PMID: 35216360 PMCID: PMC8876724 DOI: 10.3390/ijms23042244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612–13,105 and 16,390–16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.
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Affiliation(s)
- Kimberly Sturk-Andreaggi
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala 751 08, Sweden; (A.A.); (U.G.)
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.D.R.); (C.M.)
- SNA International, LLC, Alexandria, VA 22314, USA
- Correspondence: (K.S.-A.); (M.A.)
| | - Joseph D. Ring
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.D.R.); (C.M.)
- SNA International, LLC, Alexandria, VA 22314, USA
| | - Adam Ameur
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala 751 08, Sweden; (A.A.); (U.G.)
| | - Ulf Gyllensten
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala 751 08, Sweden; (A.A.); (U.G.)
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria; (M.B.); (W.P.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria; (M.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.D.R.); (C.M.)
- SNA International, LLC, Alexandria, VA 22314, USA
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
| | - Marie Allen
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala 751 08, Sweden; (A.A.); (U.G.)
- Correspondence: (K.S.-A.); (M.A.)
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7
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García Ó, Alonso S, Huber N, Bodner M, Parson W. Forensically relevant phylogeographic evaluation of mitogenome variation in the Basque Country. Forensic Sci Int Genet 2020; 46:102260. [PMID: 32062111 DOI: 10.1016/j.fsigen.2020.102260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/26/2019] [Accepted: 02/01/2020] [Indexed: 11/19/2022]
Abstract
The Basque Country has been the focus of population (genetic) and evolutionary studies for decades, as it represents an interesting evolutionary feature: it is the only European country where a non-Indo-European language is still spoken today and, for which there are no known living or extinct relatives. Early studies that were based on anatomical and serological methods, along with subsequent molecular genetic investigations, contain controversial interpretations of their data. Additionally, the analysis of mitochondrial DNA, which is maternally inherited and thus suitable for the examination of the maternal phylogeny of the population, was the focus of some studies. Early mtDNA studies were however restricted to the information provided by the control region or its hypervariable segments only. These are known to harbour little phylogenetic information, particularly for haplogroup H that is dominant in Westeurasian populations including the Basques. Later studies analysed complete mitogenome sequences. Their information content is however limited, either because the number of samples was low, or because these studies only considered particular haplogroups. In this study we present the full mitogenome sequences of 178 autochthonous Basque individuals that were carefully selected based on their familial descent and discuss the observed phylogenetic signals in the light of earlier published findings. We confirm the presence of Basque-specific mtDNA lineages and extend the knowledge of these lineages by providing data on their distribution in comparison to other Basque and non-Basque populations. This dataset improves our understanding of the Basque mtDNA phylogeny and serves as a high-quality dataset that is provided via EMPOP for forensic genetic purposes.
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Affiliation(s)
- Óscar García
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio (Bizkaia), Spain.
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Spain.
| | - Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - Martin Bodner
- 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, Pennsylvania, USA.
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8
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Smart U, Budowle B, Ambers A, Soares Moura-Neto R, Silva R, Woerner AE. A novel phylogenetic approach for de novo discovery of putative nuclear mitochondrial (pNumt) haplotypes. Forensic Sci Int Genet 2019; 43:102146. [DOI: 10.1016/j.fsigen.2019.102146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022]
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9
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Brandhagen MD, Just RS, Irwin JA. Validation of NGS for mitochondrial DNA casework at the FBI Laboratory. Forensic Sci Int Genet 2019; 44:102151. [PMID: 31629185 DOI: 10.1016/j.fsigen.2019.102151] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/09/2023]
Abstract
As a first step towards integrating next generation sequencing (NGS) technology into the FBI Laboratory's operational casework, the PowerSeq™ CRM Nested System, an NGS-based mitochondrial DNA (mtDNA) control region assay, was developmentally and internally validated. The validation studies were conducted in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) Validation Guidelines for Forensic DNA Analysis Methods, and the FBI's Quality Assurance Standards (QAS) for Forensic DNA Testing Laboratories. The assay was shown to be highly reproducible, with variant frequencies across intra and inter-run replicates of the same sample differing, on average, by just 0.3% for substitutions and point heteroplasmies and 1.5% for insertions and deletions. The assay was also shown to be extremely sensitive, yielding complete control region sequence data from as few as 2000 copies of mtDNA. This is a more than 20-fold increase in sensitivity when compared to the FBI Laboratory's current Sanger sequencing-based protocols and, based on mtDNA quantitation values of samples routinely encountered in mtDNA casework, suggests that the percentage of questioned samples from which full control region data can be recovered will increase from our current 20% to approximately 90% success with NGS technology. In addition, the assay requires on average only 30% of the extract volume typically required to develop control region profiles from degraded samples via Sanger sequencing. Overall, these studies establish the reliability of the PowerSeq™ CRM Nested System for accurate mtDNA control region typing and can serve as a model for laboratories seeking to validate NGS protocols for forensic mtDNA analysis.
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Affiliation(s)
| | - Rebecca S Just
- FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Jodi A Irwin
- FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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10
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Analysis of the mitochondrial CYTB gene sequence in human populations of northeastern Bosnia. ANTHROPOLOGICAL REVIEW 2019. [DOI: 10.2478/anre-2019-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study offers the first report on variation sequence of the mitochondrial cytochrome b (MTCYTB) gene in populations from Bosnia (northeastern Bosnia). This study was designed on the analysis of the genetic diversity of two populations of different cultural-anthropological and genetic origin, Roma population and native/non-Roma population. The main aim of our study was to estimate the usefulness of the CYTB sequence in the analysis of genetic categorization of different populations and intergroup diversity, as well as to provide some additional information on haplogroup-associated polymorphisms within the CYTB region in defining haplogroup status. Estimation of the genetic diversity was done using intra and intergroup genetic indices. The population-specific polymorphisms have been found in both categories of the populations. The results of the analysis of genetic differentiation show significant pairwise Fst differences between the Romani and native populations. Also, registered significant genetic differentiation is illustrated on the level of genetic variation between subpopulations of the Roma and non-Roma origin. The important result in our study is the confirmation of the significance of the triad of polymorphisms T14783C-G15043A-G15301A, indicating the influence of Asian component of the maternal gene pool on the genetic structure of the studied population of the Roma. Our data show that the haplogroup polymorphisms exist in the CYTB region and can provide useful information on the haplogroups that were defined only by the control region of the mtDNA. The results of this study indicate the region of CYTB gene can be a benefit in providing some additional information in the analysis of genetic structure of human populations and can be additionally applied in population studies.
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11
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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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12
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Wesselink M, Desmyter S, Kuiper I. Local populations and inaccuracies: Determining the relevant mitochondrial haplotype distributions for North West European cats. Forensic Sci Int Genet 2017. [DOI: 10.1016/j.fsigen.2017.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Lindberg MR, Schmedes SE, Hewitt FC, Haas JL, Ternus KL, Kadavy DR, Budowle B. A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes. PLoS One 2016; 11:e0167600. [PMID: 27936026 PMCID: PMC5147911 DOI: 10.1371/journal.pone.0167600] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes.
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Affiliation(s)
| | - Sarah E. Schmedes
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | | | - Jamie L. Haas
- Signature Science, LLC, Austin, Texas, United States of America
| | | | - Dana R. Kadavy
- Signature Science, LLC, Austin, Texas, United States of America
| | - Bruce Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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14
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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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15
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The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea. BIOMED RESEARCH INTERNATIONAL 2015; 2015:850648. [PMID: 26345190 PMCID: PMC4544719 DOI: 10.1155/2015/850648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/16/2015] [Indexed: 11/18/2022]
Abstract
Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods.
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16
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Complete mitochondrial genome database and standardized classification system for Canis lupus familiaris. Forensic Sci Int Genet 2015. [PMID: 26218982 DOI: 10.1016/j.fsigen.2015.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To contribute to the complete mitogenome database of the species Canis lupus familiaris and shed more light on its origin, we have sequenced mitochondrial genomes of 120 modern dogs from worldwide populations. Together with all the previously published mitogenome sequences of acceptable quality, we have reconstructed a global phylogenetic tree of 555 C. l. familiaris mitogenomes and standardized haplogroup nomenclature. The phylogenetic tree presented here and available online at http://clf.mtdna.tree.cm.umk.pl/ could be further used by forensic and evolutionary geneticists as well cynologists, for data quality control and unambiguous haplogroup classification. Our in-depth phylogeographic analysis of all C. l. familiaris mitogenomes confirmed that domestic dogs may have originated in East Asia during the Mesolithic and Upper Paleolithic time periods and started to expand to other parts of the world during Neolithic times.
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17
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Yao YG, Kajigaya S, Young NS. Mitochondrial DNA mutations in single human blood cells. Mutat Res 2015; 779:68-77. [PMID: 26149767 DOI: 10.1016/j.mrfmmm.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 01/07/2023]
Abstract
Determination mitochondrial DNA (mtDNA) sequences from extremely small amounts of DNA extracted from tissue of limited amounts and/or degraded samples is frequently employed in medical, forensic, and anthropologic studies. Polymerase chain reaction (PCR) amplification followed by DNA cloning is a routine method, especially to examine heteroplasmy of mtDNA mutations. In this review, we compare the mtDNA mutation patterns detected by three different sequencing strategies. Cloning and sequencing methods that are based on PCR amplification of DNA extracted from either single cells or pooled cells yield a high frequency of mutations, partly due to the artifacts introduced by PCR and/or the DNA cloning process. Direct sequencing of PCR product which has been amplified from DNA in individual cells is able to detect the low levels of mtDNA mutations present within a cell. We further summarize the findings in our recent studies that utilized this single cell method to assay mtDNA mutation patterns in different human blood cells. Our data show that many somatic mutations observed in the end-stage differentiated cells are found in hematopoietic stem cells (HSCs) and progenitors within the CD34(+) cell compartment. Accumulation of mtDNA variations in the individual CD34+ cells is affected by both aging and family genetic background. Granulocytes harbor higher numbers of mutations compared with the other cells, such as CD34(+) cells and lymphocytes. Serial assessment of mtDNA mutations in a population of single CD34(+) cells obtained from the same donor over time suggests stability of some somatic mutations. CD34(+) cell clones from a donor marked by specific mtDNA somatic mutations can be found in the recipient after transplantation. The significance of these findings is discussed in terms of the lineage tracing of HSCs, aging effect on accumulation of mtDNA mutations and the usage of mtDNA sequence in forensic identification.
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Affiliation(s)
- Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China.
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
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18
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Just RS, Irwin JA, Parson W. Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing. Forensic Sci Int Genet 2015; 18:131-9. [PMID: 26009256 PMCID: PMC4550493 DOI: 10.1016/j.fsigen.2015.05.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/24/2015] [Accepted: 05/05/2015] [Indexed: 12/12/2022]
Abstract
Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Well vetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10-20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method.
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Affiliation(s)
- Rebecca S Just
- Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, Dover, DE, USA; American Registry of Pathology, Rockville, MD, USA
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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19
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Skonieczna K, Malyarchuk B, Jawień A, Marszałek A, Banaszkiewicz Z, Jarmocik P, Borcz M, Bała P, Grzybowski T. Heteroplasmic substitutions in the entire mitochondrial genomes of human colon cells detected by ultra-deep 454 sequencing. Forensic Sci Int Genet 2015; 15:16-20. [DOI: 10.1016/j.fsigen.2014.10.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/20/2014] [Accepted: 10/20/2014] [Indexed: 02/03/2023]
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20
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Phylogenetic analysis of two haploid markers of 500-years-old human remains found in a central region of Korea. Genes Genomics 2015. [DOI: 10.1007/s13258-014-0226-5] [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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21
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Huber KT, Van Iersel L, Moulton V, Wu T. How much information is needed to infer reticulate evolutionary histories? Syst Biol 2014; 64:102-11. [PMID: 25236959 PMCID: PMC4265143 DOI: 10.1093/sysbio/syu076] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Phylogenetic networks are a generalization of evolutionary trees and are an important tool for analyzing reticulate evolutionary histories. Recently, there has been great interest in developing new methods to construct rooted phylogenetic networks, that is, networks whose internal vertices correspond to hypothetical ancestors, whose leaves correspond to sampled taxa, and in which vertices with more than one parent correspond to taxa formed by reticulate evolutionary events such as recombination or hybridization. Several methods for constructing evolutionary trees use the strategy of building up a tree from simpler building blocks (such as triplets or clusters), and so it is natural to look for ways to construct networks from smaller networks. In this article, we shall demonstrate a fundamental issue with this approach. Namely, we show that even if we are given all of the subnetworks induced on all proper subsets of the leaves of some rooted phylogenetic network, we still do not have all of the information required to completely determine that network. This implies that even if all of the building blocks for some reticulate evolutionary history were to be taken as the input for any given network building method, the method might still output an incorrect history. We also discuss some potential consequences of this result for constructing phylogenetic networks.
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Affiliation(s)
- Katharina T Huber
- School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands
| | - Leo Van Iersel
- School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands
| | - Taoyang Wu
- School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands
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22
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Zimmermann B, Rock AW, Dur A, Parson W. Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software. Croat Med J 2014; 55:115-20. [PMID: 24778097 PMCID: PMC4020147 DOI: 10.3325/cmj.2014.55.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Aim To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors. Method We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; www.empop.org) by means of two mtDNA data sets that were submitted for quality control. Results The quasi-median network torsi of the two data sets resulted in complex reticulations, suggesting ambiguous data. To check the corresponding raw data, accountable nodes and connecting branches of the network could be identified by highlighting induced subgraphs with concurrent dimming of their complements. This is achieved by accentuating the relevant substructures in the network: mouse clicking on a node displays a list of all mtDNA haplotypes included in that node; the selection of a branch specifies the mutation(s) connecting two nodes. It is indicated to evaluate these mutations by means of the raw data. Conclusion Inspection of the raw data confirmed the presence of phantom mutations due to suboptimal electrophoresis conditions and data misinterpretation. The network software proved to be a powerful tool to highlight problematic data and guide quality control of mtDNA data tables.
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Affiliation(s)
| | | | | | - Walther Parson
- Walther Parson, Institute of Legal Medicine, Medical University, Mullerstrasse 44, A-6020 Innsbruck, Austria,
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23
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High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq. Forensic Sci Int Genet 2014; 12:128-35. [DOI: 10.1016/j.fsigen.2014.06.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/29/2014] [Accepted: 06/01/2014] [Indexed: 12/21/2022]
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24
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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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25
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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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26
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Forensic strategy to ensure the quality of sequencing data of mitochondrial DNA in highly degraded samples. Leg Med (Tokyo) 2014; 16:52-5. [DOI: 10.1016/j.legalmed.2013.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/18/2013] [Accepted: 10/04/2013] [Indexed: 11/23/2022]
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27
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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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28
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Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut FX, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza LP, Champion B, Dugoujon JM. Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One 2013; 8:e80932. [PMID: 24278350 PMCID: PMC3838347 DOI: 10.1371/journal.pone.0080932] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.
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Affiliation(s)
- Mélanie Capredon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
- Department of Pediatrics, CHU Sainte Justine, Faculty of Medecine, University of Montreal, Quebec, Canada
- *
| | - Nicolas Brucato
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Laure Tonasso
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Valérie Choesmel-Cadamuro
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - François-Xavier Ricaut
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Harilanto Razafindrazaka
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | | | - Mamisoa Adelta Ratolojanahary
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Louis-Paul Randriamarolaza
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Bernard Champion
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
| | - Jean-Michel Dugoujon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
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29
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Can the occurrence of rare insertion/deletion polymorphisms in human mtDNA be verified from phylogeny? Sci Bull (Beijing) 2013. [DOI: 10.1007/bf03325651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Fan L, Yao YG. An update to MitoTool: using a new scoring system for faster mtDNA haplogroup determination. Mitochondrion 2013; 13:360-3. [PMID: 23632257 DOI: 10.1016/j.mito.2013.04.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 03/05/2013] [Accepted: 04/19/2013] [Indexed: 11/17/2022]
Abstract
The determination of human mitochondrial DNA (mtDNA) haplogroups is not only crucial in anthropological and forensic studies, but is also helpful in the medical field to prevent establishment of wrong disease associations. In recent years, high-throughput technologies and the huge amounts of data they create, as well as the regular updates to the mtDNA phylogenetic tree, mean that there is a need for an automated approach which can make a speedier determination of haplogroups than can be made by using the traditional manual method. Here, we update the MitoTool (www.mitotool.org) by incorporating a novel scoring system for the determination of mtDNA into haplogroups, which has advantages on speed, accuracy and ease of implementation. In order to make the access to MitoTool easier, we also provide a stand-alone version of the program that will run on a local computer and this version is freely available at the MitoTool website.
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Affiliation(s)
- Long Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
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31
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Parr RL, Jakupciak JP, Birch-Machin MA, Dakubo GD. The mitochondrial genome: a biosensor for early cancer detection? ACTA ACUST UNITED AC 2013; 1:169-82. [PMID: 23489304 DOI: 10.1517/17530059.1.2.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mutations in the mitochondrial genome have been reported as biomarkers for the detection of cancer. Hallmarks of cancer development include the accumulation of genetic alterations in the mitochondrial and nuclear genomes. Damage to mitochondria affects energy metabolism, generation of reactive oxygen species, apoptosis, cell growth and other processes that contribute to the neoplastic process. Furthermore, mitochondrial DNA mutations occur frequently in cancer. Little work has been done to link a pathway between mitochondrial mutations and cancer etiology. Volumes of work have been reported on the association of mitochondrial mutations and almost all types of cancer including the use of body fluids for early detection. This review examines the measurement of mitochondrial mutations for the application of detecting human tumor tissue.
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Affiliation(s)
- Ryan L Parr
- Vice President of Research, Genesis Genomics, Inc., 290 Munro Street, Ste 1000, Thunder Bay, Ontario, P7A 7T1, Canada +1 807 346 8100; +1 807 346 8105 ;
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32
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Yu M, Wan Y, Zou Q. Somatic mitochondrial DNA mutations in Chinese patients with osteosarcoma. Int J Exp Pathol 2013; 94:126-32. [PMID: 23441585 DOI: 10.1111/iep.12015] [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: 11/15/2012] [Accepted: 12/15/2012] [Indexed: 12/13/2022] Open
Abstract
Somatic mutations in mitochondrial DNA (mtDNA) have been long proposed to drive the pathogenesis and progression of human malignancies. Previous investigations have revealed a high frequency of somatic mutations in the D-loop control region of mtDNA in osteosarcoma. However, little is known with regard to whether or not somatic mutations also occur in the coding regions of mtDNA in osteosarcoma. To test this possibility, in the present study we screened somatic mutations over the full-length mitochondrial genome of 31 osteosarcoma tumour tissue samples, and corresponding peripheral blood samples from the same cohort of patients. We detected a sum of 11 somatic mutations in the mtDNA coding regions in our series. Nine of them were missense or frameshift mutations that have the potential to hamper mitochondrial respiratory function. In combination with our earlier observations on the D-loop fragment, 71.0% (22/31) of patients with osteosarcoma carried at least one somatic mtDNA mutation, and a total of 40 somatic mutations were identified. Amongst them, 29 (72.5%) were located in the D-loop region, two (5%) were in the sequences of the tRNA genes, two (5%) were in the mitochondrial ATP synthase subunit 6 gene and seven (17.5%) occurred in genes encoding components of the mitochondrial respiratory complexes. In addition, somatic mtDNA mutation was not closely associated with the clinicopathological characteristics of osteosarcoma. Together, these findings suggest that somatic mutations are highly prevalent events in both coding and non-coding regions of mtDNA in osteosarcoma. Some missense and frameshift mutations are putatively harmful to proper mitochondrial activity and might play vital roles in osteosarcoma carcinogenesis.
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Affiliation(s)
- Man Yu
- Ontario Cancer Institute/Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, ON, Canada
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33
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Behar D, van Oven M, Rosset S, Metspalu M, Loogväli EL, Silva N, Kivisild T, Torroni A, Villems R. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet 2012; 90:675-84. [PMID: 22482806 PMCID: PMC3322232 DOI: 10.1016/j.ajhg.2012.03.002] [Citation(s) in RCA: 316] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 02/22/2012] [Accepted: 03/02/2012] [Indexed: 11/19/2022] Open
Abstract
Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations, and errors in medical, forensic, and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence, which was identified by considering all available mitogenomes from Homo neanderthalensis. This "Copernican" reassessment of the human mtDNA tree from its deepest root should resolve previous problems and will have a substantial practical and educational influence on the scientific and public perception of human evolution by clarifying the core principles of common ancestry for extant descendants.
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Affiliation(s)
- Doron M. Behar
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
- Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel
| | - Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Saharon Rosset
- Department of Statistics and Operations Research, School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mait Metspalu
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Eva-Liis Loogväli
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Nuno M. Silva
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto 4200-465, Portugal
| | - Toomas Kivisild
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
- Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani,” Università di Pavia, Pavia 27100, Italy
| | - Richard Villems
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
- Estonian Academy of Sciences, 6 Kohtu Street, Tallinn 10130, Estonia
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Comparative evolution of S7 Intron 1 and ribosomal internal transcribed spacer in Coilia nasus (Clupeiformes: Engraulidae). Int J Mol Sci 2012; 13:3085-3100. [PMID: 22489143 PMCID: PMC3317704 DOI: 10.3390/ijms13033085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 01/17/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022] Open
Abstract
Coilia nasus is widely distributed in the Yangtze River, the coastal waters of China, Korea and the Ariake Sound of Japan. Several ecotypes exist and this provides a useful model for the study of comparative diversity between molecular markers. Here we analyze and compare the nucleotide sequences between single-copy ribosomal protein S7 gene intron 1 (rpS7) and multiple-copy ribosomal internal transcribed spacer 1 (ITS1) in this species to compare the phylogenetic signal of the two nuclear genes. Nucleotide substitutions among the two gene sequences and partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) gene were also analyzed. A total of 115 clones for rpS7 and 122 clones for ITS1 were obtained from 37 specimens. The nucleotide sequence length is 741 to 743 bp for rpS7 and 334 to 348 bp for ITS1. Intra- and inter-specimen variation in rpS7 results from nucleotide substitution, while such variation in ITS1 is mainly due to different numbers of short base repeats. The content of G + C is lower in rpS7 (43.5%) than in ITS1 (68.2%). Our results indicate that the proportion of the sequence variable sites is higher in rpS7 (61) than in ITS1 (23); the informative parsimony of rpS7 is evidently higher than that of ITS1 (26 vs. 2); the overall ratio between transitions and transversions in ITS1 is slightly lower than in rpS7, but remarkably lower than in COI. These results suggest that rpS7 is more suitable than ITS1 as a marker for genetic divergence of this group. Furthermore, gene flow is observed between the different geographic populations of C. nasus from the phylogeny of this species based on rpS7, showing that rpS7 has more evolutionary characteristics for understanding the processes of genomic evolution at the intraspecific level.
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Marquez MC. Interpretation guidelines of mtDNA control region sequence electropherograms in forensic genetics. Methods Mol Biol 2012; 830:301-319. [PMID: 22139669 DOI: 10.1007/978-1-61779-461-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Forensic mitochondrial DNA (mtDNA) analysis is a complementary technique to forensic nuclear DNA (nDNA) and trace evidence analysis. Its use has been accepted by the vast majority of courts of law around the world. However for the forensic community it is crucial to employ standardized methods and procedures to guaranty the quality of the results obtained in court. In this chapter, we describe the most important aspects regarding the interpretation and assessment of mtDNA analysis, and offer a simple guide which places particular emphasis on those aspects that can impact the final interpretation of the results. These include the criteria for authenticating a sequence excluding the contaminant origin, defining the quality of a sequence, editing procedure, alignment criteria for searching the databases, and the statistical evaluation of matches. It is not easy to establish a single guide to interpretation for mtDNA analysis; however, it is important to understand all variables that may in some way affect the final conclusion in the context of a forensic case. As a general rule, laboratories should be cautious before issuing the final conclusion of an mtDNA analysis, and consider any significant limitations regarding current understanding of specific aspects of the mtDNA molecule.
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Montesino M, Prieto L. Capillary electrophoresis of Big-Dye terminator sequencing reactions for human mtDNA Control Region haplotyping in the identification of human remains. Methods Mol Biol 2012; 830:267-281. [PMID: 22139667 DOI: 10.1007/978-1-61779-461-2_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cycle sequencing reaction with Big-Dye terminators provides the methodology to analyze mtDNA Control Region amplicons by means of capillary electrophoresis. DNA sequencing with ddNTPs or terminators was developed by (1). The progressive automation of the method by combining the use of fluorescent-dye terminators with cycle sequencing has made it possible to increase the sensibility and efficiency of the method and hence has allowed its introduction into the forensic field. PCR-generated mitochondrial DNA products are the templates for sequencing reactions. Different set of primers can be used to generate amplicons with different sizes according to the quality and quantity of the DNA extract providing sequence data for different ranges inside the Control Region.
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Affiliation(s)
- Marta Montesino
- Comisaría General de Policía Científica, Servicio de Analítica, Laboratorio de ADN, Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Madrid, 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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Wang CY, Zhao ZB. Somatic mtDNA mutations in lung tissues of pesticide-exposed fruit growers. Toxicology 2012; 291:51-5. [DOI: 10.1016/j.tox.2011.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 10/12/2011] [Accepted: 10/27/2011] [Indexed: 12/24/2022]
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Skonieczna K, Malyarchuk BA, Grzybowski T. The landscape of mitochondrial DNA variation in human colorectal cancer on the background of phylogenetic knowledge. Biochim Biophys Acta Rev Cancer 2011; 1825:153-9. [PMID: 22178219 DOI: 10.1016/j.bbcan.2011.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/21/2011] [Accepted: 11/23/2011] [Indexed: 01/07/2023]
Abstract
Recently, an increasing number of studies indicate that mutations in mitochondrial genome may contribute to cancer development or metastasis. Hence, it is important to determine whether the mitochondrial DNA might be a good, clinically applicable marker of cancer. This review describes hereditary as well as somatic mutations reported in mitochondrial DNA of colorectal cancer cells. We showed here that the entire mitochondrial genome mutational spectra are different in colorectal cancer and non-tumor cells. We also placed the described mutations on the phylogenetic context, which highlighted the recurrent problem of data quality. Therefore, the most important rules for adequately assessing the quality of mitochondrial DNA sequence analysis in cancer have been summarized. As follows from this review, neither the reliable spectrum of mtDNA somatic mutations nor the association between hereditary mutations and colorectal cancer risk have been resolved. This indicates that only high resolution studies on mtDNA variability, followed by a proper data interpretation employing phylogenetic knowledge may finally verify the utility of mtDNA sequence (if any) in clinical practice.
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Affiliation(s)
- Katarzyna Skonieczna
- Department of Molecular and Forensic Genetics, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Sklodowskiej-Curie Street, 85-094 Bydgoszcz, Poland
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Liu J, Wang LD, Sun YB, Li EM, Xu LY, Zhang YP, Yao YG, Kong QP. Deciphering the Signature of Selective Constraints on Cancerous Mitochondrial Genome. Mol Biol Evol 2011; 29:1255-61. [DOI: 10.1093/molbev/msr290] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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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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The awakening of an advanced malignant cancer: an insult to the mitochondrial genome. Biochim Biophys Acta Gen Subj 2011; 1820:652-62. [PMID: 21920409 DOI: 10.1016/j.bbagen.2011.08.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 08/26/2011] [Accepted: 08/29/2011] [Indexed: 02/08/2023]
Abstract
BACKGROUND In only months-to-years a primary cancer can progress to an advanced phenotype that is metastatic and resistant to clinical treatments. As early as the 1900s, it was discovered that the progression of a cancer to the advanced phenotype is often associated with a shift in the metabolic profile of the disease from a state of respiration to anaerobic fermentation - a phenomenon denoted as the Warburg Effect. SCOPE OF REVIEW Reports in the literature strongly suggest that the Warburg Effect is generated as a response to a loss in the integrity of the sequence and/or copy number of the mitochondrial genome content within a cancer. MAJOR CONCLUSIONS Multiple studies regarding the progression of cancer indicate that mutation, and/or, a flux in the copy number, of the mitochondrial genome content can support the early development of a cancer, until; the mutational load and/or the reduction-to-depletion of the copy number of the mitochondrial genome content induces the progression of the disease to an advanced phenotype. GENERAL SIGNIFICANCE Collectively, evidence has revealed that the human cell has incorporated the mitochondrial genome content into a cellular mechanism that, when pathologically actuated, can de(un)differentiate a cancer from the parental tissue of origin into an autonomous disease that disrupts the hierarchical structure-and-function of the human body. This article is part of a Special Issue entitled: Biochemistry of Mitochondria.
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Wang CY, Li H, Hao XD, Liu J, Wang JX, Wang WZ, Kong QP, Zhang YP. Uncovering the profile of somatic mtDNA mutations in Chinese colorectal cancer patients. PLoS One 2011; 6:e21613. [PMID: 21738732 PMCID: PMC3125228 DOI: 10.1371/journal.pone.0021613] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 06/03/2011] [Indexed: 12/20/2022] Open
Abstract
In the past decade, a high incidence of somatic mitochondrial DNA (mtDNA) mutations has been observed, mostly based on a fraction of the molecule, in various cancerous tissues; nevertheless, some of them were queried due to problems in data quality. Obviously, without a comprehensive understanding of mtDNA mutational profile in the cancerous tissue of a specific patient, it is unlikely to disclose the genuine relationship between somatic mtDNA mutations and tumorigenesis. To achieve this objective, the most straightforward way is to directly compare the whole mtDNA genome variation among three tissues (namely, cancerous tissue, para-cancerous tissue, and distant normal tissue) from the same patient. Considering the fact that most of the previous studies on the role of mtDNA in colorectal tumor focused merely on the D-loop or partial segment of the molecule, in the current study we have collected three tissues (cancerous, para-cancerous and normal tissues) respectively recruited from 20 patients with colorectal tumor and completely sequenced the mitochondrial genome of each tissue. Our results reveal a relatively lower incidence of somatic mutations in these patients; intriguingly, all somatic mutations are in heteroplasmic status. Surprisingly, the observed somatic mutations are not restricted to cancer tissues, for the para-cancer tissues and distant normal tissues also harbor somatic mtDNA mutations with a lower frequency than cancerous tissues but higher than that observed in the general population. Our results suggest that somatic mtDNA mutations in cancerous tissues could not be simply explained as a consequence of tumorigenesis; meanwhile, the somatic mtDNA mutations in normal tissues might reflect an altered physiological environment in cancer patients.
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Affiliation(s)
- Cheng-Ye Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hui Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Dan Hao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Jia Liu
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
| | - Jia-Xin Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- * E-mail: (Y-PZ); (Q-PK)
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- * E-mail: (Y-PZ); (Q-PK)
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Abstract
BACKGROUND The assignment of DNA samples to coarse population groups can be a useful but difficult task. One such example is the inference of coarse ethnic groupings for forensic applications. Ethnicity plays an important role in forensic investigation and can be inferred with the help of genetic markers. Being maternally inherited, of high copy number, and robust persistence in degraded samples, mitochondrial DNA may be useful for inferring coarse ethnicity. In this study, we compare the performance of methods for inferring ethnicity from the sequence of the hypervariable region of the mitochondrial genome. RESULTS We present the results of comprehensive experiments conducted on datasets extracted from the mtDNA population database, showing that ethnicity inference based on support vector machines (SVM) achieves an overall accuracy of 80-90%, consistently outperforming nearest neighbor and discriminant analysis methods previously proposed in the literature. We also evaluate methods of handling missing data and characterize the most informative segments of the hypervariable region of the mitochondrial genome. CONCLUSIONS Support vector machines can be used to infer coarse ethnicity from a small region of mitochondrial DNA sequence with surprisingly high accuracy. In the presence of missing data, utilizing only the regions common to the training sequences and a test sequence proves to be the best strategy. Given these results, SVM algorithms are likely to also be useful in other DNA sequence classification applications.
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Affiliation(s)
- Chih Lee
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Ion I Măndoiu
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Craig E Nelson
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT, USA
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Yang Y, Zhang P, He Q, Zhu Y, Yang X, Lv R, Chen J. A new strategy for the discrimination of mitochondrial DNA haplogroups in Han population. J Forensic Sci 2011; 56:586-90. [PMID: 21470221 DOI: 10.1111/j.1556-4029.2011.01711.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mitochondrial DNA (mtDNA) haplogroup discrimination is interesting not only for phylogenetic and clinical but also for forensic studies. We discriminated the mtDNA haplogroups of 570 healthy unrelated Han people from Zhejiang Province, Southeast China, by comprehensive analysis mutations of the hypervariable segments-I sequence and diagnostic polymorphisms in mtDNA coding region using real-time polymerase chain reaction (RT-PCR), which was compared with the widely used PCR and restriction fragment length polymorphism (PCR-RFLP) method. The results showed that in superhaplogroup M, haplogroup D was the most common haplotype within this assay to 24.6%, and in the other superhaplotype N, haplogroup B and F were the most common groups. Samples re-identified by PCR-RFLP showed the consistent results that were got with RT-PCR. In conclusion, the RT-PCR strategy appears to be an accurate, reproducible, and sensitive technique for the discrimination of mtDNA haplogroups, especially for mass screenings quickly and economically.
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Affiliation(s)
- Yi Yang
- Kidney Disease Center, First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China
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46
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Gayà-Vidal M, Moral P, Saenz-Ruales N, Gerbault P, Tonasso L, Villena M, Vasquez R, Bravi CM, Dugoujon JM. mtDNA and Y-chromosome diversity in Aymaras and Quechuas from Bolivia: Different stories and special genetic traits of the Andean Altiplano populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 145:215-30. [DOI: 10.1002/ajpa.21487] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 12/09/2010] [Indexed: 11/11/2022]
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47
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Czarnecka AM, Bartnik E. The role of the mitochondrial genome in ageing and carcinogenesis. J Aging Res 2011; 2011:136435. [PMID: 21403887 PMCID: PMC3042732 DOI: 10.4061/2011/136435] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 01/03/2011] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial DNA mutations and polymorphisms have been the focus of intensive investigations for well over a decade in an attempt to understand how they affect fundamental processes such as cancer and aging. Initial interest in mutations occurring in mitochondrial DNA of cancer cells diminished when most were found to be the same mutations which occurred during the evolution of human mitochondrial haplogroups. However, increasingly correlations are being found between various mitochondrial haplogroups and susceptibility to cancer or diseases in some cases and successful aging in others.
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Affiliation(s)
- Anna M. Czarnecka
- Laboratory of Molecular Oncology, Department of Oncology, Military Institute of Medicine, ul. Szaserów 128, 01-141 Warsaw, Poland
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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48
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Liu C, Wang SY, Zhao M, Xu ZY, Hu YH, Chen F, Zhang RZ, Gao GF, Yu YS, Kong QP. Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China. Forensic Sci Int Genet 2011; 5:e4-10. [DOI: 10.1016/j.fsigen.2010.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 04/14/2010] [Accepted: 04/24/2010] [Indexed: 10/19/2022]
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49
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Kloss-Brandstätter A, Pacher D, Schönherr S, Weissensteiner H, Binna R, Specht G, Kronenberg F. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum Mutat 2010; 32:25-32. [PMID: 20960467 DOI: 10.1002/humu.21382] [Citation(s) in RCA: 354] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 09/16/2010] [Indexed: 01/02/2023]
Abstract
An ongoing source of controversy in mitochondrial DNA (mtDNA) research is based on the detection of numerous errors in mtDNA profiles that led to erroneous conclusions and false disease associations. Most of these controversies could be avoided if the samples' haplogroup status would be taken into consideration. Knowing the mtDNA haplogroup affiliation is a critical prerequisite for studying mechanisms of human evolution and discovering genes involved in complex diseases, and validating phylogenetic consistency using haplogroup classification is an important step in quality control. However, despite the availability of Phylotree, a regularly updated classification tree of global mtDNA variation, the process of haplogroup classification is still time-consuming and error-prone, as researchers have to manually compare the polymorphisms found in a population sample to those summarized in Phylotree, polymorphism by polymorphism, sample by sample. We present HaploGrep, a fast, reliable and straight-forward algorithm implemented in a Web application to determine the haplogroup affiliation of thousands of mtDNA profiles genotyped for the entire mtDNA or any part of it. HaploGrep uses the latest version of Phylotree and offers an all-in-one solution for quality assessment of mtDNA profiles in clinical genetics, population genetics and forensics. HaploGrep can be accessed freely at http://haplogrep.uibk.ac.at.
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Affiliation(s)
- Anita Kloss-Brandstätter
- Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Austria.
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50
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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: 31] [Impact Index Per Article: 2.2] [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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