Mitochondrial DNA in human identification: a review

Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensicsamples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of human identification focusing on the most relevant issues for the forensic and medico-legal areas.

[1]  Walther Parson,et al.  Forensic Population Genetics - Original Research Full mtGenome reference data: Development and characterization of 588 forensic-quality haplotypes representing three U.S. populations , 2015 .

[2]  Bruce Budowle,et al.  A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis , 2017, PloS one.

[3]  António Amorim,et al.  Big data in forensic genetics. , 2018, Forensic science international. Genetics.

[4]  M. Stoneking,et al.  Mitochondrial DNA and human evolution , 1987, Nature.

[5]  Holly M. Mortensen,et al.  Whole-mtDNA genome sequence analysis of ancient African lineages. , 2007, Molecular biology and evolution.

[6]  D. Ballard.  Analysis of Mitochondrial Control Region Using Sanger Sequencing. , 2016, Methods in molecular biology.

[7]  Y. Chien,et al.  Biparental Inheritance of Mitochondrial DNA in Humans , 2018, Proceedings of the National Academy of Sciences.

[8]  Yu Cao,et al.  Massive parallel sequencing of mitochondrial DNA genomes from mother-child pairs using the ion torrent personal genome machine (PGM). , 2018, Forensic science international. Genetics.

[9]  August E. Woerner,et al.  Evaluation of the precision ID mtDNA whole genome panel on two massively parallel sequencing systems. , 2018, Forensic science international. Genetics.

[10]  Rebecca S. Just,et al.  Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing , 2015, Forensic science international. Genetics.

[11]  B. Sykes,et al.  Length heteroplasmy in the first hypervariable segment of the human mtDNA control region. , 1995, American journal of human genetics.

[12]  J. Lee,et al.  Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population , 2017, Journal of Korean medical science.

[13]  Walther Parson,et al.  Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)☆ , 2013, Forensic science international. Genetics.

[14]  Jennifer D. Churchill,et al.  More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing , 2016, BMC Genomics.

[15]  Li Li,et al.  Preliminary DNA Identification for the Tsunami Victims in Thailand , 2016, Genomics, proteomics & bioinformatics.

[16]  Robert J. Goodloe,et al.  Characterization of mitochondrial haplogroups in a large population-based sample from the United States , 2014, Human Genetics.

[17]  Mannis van Oven,et al.  PhyloTree Build 17: Growing the human mitochondrial DNA tree , 2015 .

[18]  W. Goodwin.  The use of forensic DNA analysis in humanitarian forensic action: The development of a set of international standards. , 2017, Forensic science international.

[19]  Pierre Baldi,et al.  An enhanced MITOMAP with a global mtDNA mutational phylogeny , 2006, Nucleic Acids Res..

[20]  Andrzej Ossowski,et al.  Genetic Identification of Communist Crimes’ Victims (1944–1956) Based on the Analysis of One of Many Mass Graves Discovered on the Powazki Military Cemetery in Warsaw, Poland , 2016, Journal of forensic sciences.

[21]  D. Wallace.  Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine. , 2007, Annual review of biochemistry.

[22]  D. Wallace,et al.  mtDNA variation in the South African Kung and Khwe-and their genetic relationships to other African populations. , 2000, American journal of human genetics.

[23]  Jiannis Ragoussis,et al.  Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations , 2016, Scientific Reports.

[24]  W. Parson,et al.  World War One Italian and Austrian soldier identification project: DNA results of the first case. , 2010, Forensic science international. Genetics.

[25]  Evaluating heteroplasmic variations of the mitochondrial genome from whole genome sequencing data. , 2019, Gene.

[26]  Martin Picard,et al.  The rise of mitochondria in medicine. , 2016, Mitochondrion.

[27]  K. Sturk-Andreaggi,et al.  Performance evaluation of a mitogenome capture and Illumina sequencing protocol using non-probative, case-type skeletal samples: Implications for the use of a positive control in a next-generation sequencing procedure. , 2017, Forensic science international. Genetics.

[28]  R. Vossen,et al.  Full-Length Mitochondrial-DNA Sequencing on the PacBio RSII. , 2017, Methods in molecular biology.

[29]  R. Yanagimachi,et al.  Fate of microinjected sperm components in the mouse oocyte and embryo , 1997, Zygote.

[30]  N. Morling,et al.  A study of the peopling of Greenland using next generation sequencing of complete mitochondrial genomes. , 2016, American journal of physical anthropology.

[31]  J. A. DiZinno,et al.  A family exhibiting heteroplasmy in the human mitochondrial DNA control region reveals both somatic mosaicism and pronounced segregation of mitotypes , 1997, Human Genetics.

[32]  M. Holland,et al.  Mitochondrial DNA regions HVI and HVII population data. , 1999, Forensic science international.

[33]  J. Poland,et al.  Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley , 2013, PloS one.

[34]  Walther Parson,et al.  EMPOP--a forensic mtDNA database. , 2007, Forensic science international. Genetics.

[35]  P. de Knijff,et al.  High-quality mtDNA control region sequences from 680 individuals sampled across the Netherlands to establish a national forensic mtDNA reference database. , 2016, Forensic science international. Genetics.

[36]  H. Yonekawa,et al.  Selective and continuous elimination of mitochondria microinjected into mouse eggs from spermatids, but not from liver cells, occurs throughout embryogenesis. , 2000, Genetics.

[37]  Walther Parson,et al.  Evaluation of the precision ID whole MtDNA genome panel for forensic analyses. , 2018, Forensic science international. Genetics.

[38]  B. Llamas,et al.  DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification , 2013, Investigative Genetics.

[39]  W R Mayr,et al.  DNA Commission of the International Society for Forensic Genetics: revised and extended guidelines for mitochondrial DNA typing. , 2014, Forensic science international. Genetics.

[40]  Jaume Bertranpetit,et al.  The dawn of human matrilineal diversity. , 2008, American journal of human genetics.

[41]  C. Hutchison,et al.  Maternal inheritance of mammalian mitochondrial DNA , 1974, Nature.

[42]  D. Turnbull,et al.  Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA , 1999, Nature Genetics.

[43]  P. Gill,et al.  Identification of the remains of the Romanov family by DNA analysis , 1994, Nature Genetics.

[44]  H. Wallace,et al.  Forensic DNA databases–Ethical and legal standards: A global review , 2014 .

[45]  Mark R. Wilson,et al.  Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set. , 2004, Legal medicine.

[46]  J. Irwin,et al.  Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq. , 2016, Forensic science international. Genetics.

[47]  J. Shendure,et al.  Materials and Methods Som Text Figs. S1 and S2 Tables S1 to S4 References Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2022 .

[48]  Lin Liu,et al.  Comparison of Next-Generation Sequencing Systems , 2012, Journal of biomedicine & biotechnology.

[49]  M. Kayser,et al.  Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine , 2015, Human mutation.

[50]  W. Parson,et al.  Is it possible to differentiate mtDNA by means of HVIII in samples that cannot be distinguished by sequencing the HVI and HVII regions? , 2000, Forensic science international.

[51]  Bernard P. Puc,et al.  An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.

[52]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[53]  A. Torroni,et al.  Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade , 2001, Annals of human genetics.

[54]  M. Stoneking,et al.  Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. , 1991, American journal of human genetics.

[55]  D. Turnbull,et al.  Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age. , 2001, American journal of human genetics.

[56]  M. M. Nass,et al.  INTRAMITOCHONDRIAL FIBERS WITH DNA CHARACTERISTICS: I. Fixation and Electron Staining Reactions , 1963 .

[57]  Brian D. Ondov,et al.  An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System , 2010, Bioinform..

[58]  M. M. Nass,et al.  INTRAMITOCHONDRIAL FIBERS WITH DNA CHARACTERISTICS , 1963, The Journal of cell biology.

[59]  B Brinkmann,et al.  Considerations by the European DNA profiling (EDNAP) group on the working practices, nomenclature and interpretation of mitochondrial DNA profiles. , 2001, Forensic science international.

[60]  Jennifer D. Churchill,et al.  Massively parallel sequencing-enabled mixture analysis of mitochondrial DNA samples , 2018, International Journal of Legal Medicine.

[61]  Katherine Geiersbach,et al.  Comparison of the Illumina Genome Analyzer and Roche 454 GS FLX for resequencing of hypertrophic cardiomyopathy-associated genes. , 2010, Journal of biomolecular techniques : JBT.

[62]  H. Yonekawa,et al.  Maternal inheritance of mouse mtDNA in interspecific hybrids: segregation of the leaked paternal mtDNA followed by the prevention of subsequent paternal leakage. , 1998, Genetics.

[63]  Walther Parson,et al.  Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA) , 2013, Forensic science international. Genetics.

[64]  Mark R. Wilson,et al.  Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set. , 2005, Forensic science international.

[65]  Pierre Baldi,et al.  MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences , 2009, Human mutation.

[66]  M. Bicalho,et al.  Mitochondrial DNA control region diversity in a population from Parana state—increasing the Brazilian forensic database , 2018, International Journal of Legal Medicine.

[67]  Manfred Kayser,et al.  Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation , 2009, Human mutation.

[68]  V. Kisand,et al.  Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology , 2015, Molecular ecology resources.

[69]  A. Torroni,et al.  Classification of European mtDNAs from an analysis of three European populations. , 1996, Genetics.

[70]  J. Attems,et al.  Mitochondrial DNA point mutations and relative copy number in 1363 disease and control human brains , 2017, Acta neuropathologica communications.

[71]  F. Sanger,et al.  Sequence and organization of the human mitochondrial genome , 1981, Nature.

[72]  A. Wilson,et al.  Paternal inheritance of mitochondrial DNA in mice , 1991, Nature.

[73]  Aylwyn Scally,et al.  The mutation rate in human evolution and demographic inference. , 2016, Current opinion in genetics & development.

[74]  A. Rakha,et al.  Mitochondrial control region diversity in Sindhi ethnic group of Pakistan. , 2017, Legal medicine.

[75]  W R Mayr,et al.  DNA Commission of the International Society for Forensic Genetics (ISFG): recommendations regarding the role of forensic genetics for disaster victim identification (DVI). , 2007, Forensic science international. Genetics.

[76]  I. Ovchinnikov,et al.  Whole Human Mitochondrial DNA Sequencing. , 2016, Methods in molecular biology.

[77]  W. Parson,et al.  The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization. , 2016, Forensic science international. Genetics.

[78]  P. Donnelly,et al.  The mutation rate in the human mtDNA control region. , 2000, American journal of human genetics.

[79]  David Balding,et al.  Identification of the remains of King Richard III , 2014, Nature Communications.

[80]  J. Taanman,et al.  The mitochondrial genome: structure, transcription, translation and replication. , 1999, Biochimica et biophysica acta.

[82]  B. Greenberg,et al.  Intraspecific nucleotide sequence variability surrounding the origin of replication in human mitochondrial DNA. , 1983, Gene.

[83]  J. Prieto,et al.  Identification process in mass graves from the Spanish Civil War I. , 2010, Forensic science international.

[84]  B. Sykes,et al.  Variable levels of a heteroplasmic point mutation in individual hair roots. , 1997, American journal of human genetics.

[85]  T. Kivisild,et al.  Maternal ancestry and population history from whole mitochondrial genomes , 2015, Investigative Genetics.

[86]  B. Ludes,et al.  Case report: on the use of the HID-Ion AmpliSeq™ Ancestry Panel in a real forensic case , 2017, International Journal of Legal Medicine.

[87]  G. Rogers.  Hair follicle differentiation and regulation. , 2004, The International journal of developmental biology.

[88]  Mark R. Wilson,et al.  Forensics and mitochondrial DNA: applications, debates, and foundations. , 2003, Annual review of genomics and human genetics.

[89]  Mark R. Wilson,et al.  Characterization of the Caucasian haplogroups present in the SWGDAM forensic mtDNA dataset for 1771 human control region sequences. Scientific Working Group on DNA Analysis Methods. , 2002, Journal of forensic sciences.

[90]  R. Paus.  Principles of Hair Cycle Control , 1998, The Journal of dermatology.

[91]  J. A. DiZinno,et al.  Length variation in HV2 of the human mitochondrial DNA control region. , 2001, Journal of forensic sciences.

[92]  Á. Carracedo,et al.  Ethical-legal problems of DNA databases in criminal investigation , 2000, Journal of medical ethics.

[93]  W. Parson,et al.  Development of forensic-quality full mtGenome haplotypes: success rates with low template specimens. , 2014, Forensic science international. Genetics.

[94]  Darren P Martin,et al.  Phylogenetic reconstruction methods: an overview. , 2014, Methods in molecular biology.

[95]  J. Puente,et al.  Identification process in mass graves from the Spanish Civil War II. , 2012, Forensic science international.

[96]  R. Villems,et al.  MtDNA Profile of West Africa Guineans: Towards a Better Understanding of the Senegambia Region , 2004, Annals of human genetics.

[97]  K. Sullivan,et al.  Identification of human remains by amplification and automated sequencing of mitochondrial DNA , 2006, International Journal of Legal Medicine.

[98]  A. Salas,et al.  Results of the 1999-2000 collaborative exercise and proficiency testing program on mitochondrial DNA of the GEP-ISFG: an inter-laboratory study of the observed variability in the heteroplasmy level of hair from the same donor. , 2002, Forensic science international.

[99]  L. Rodella,et al.  The human hair: from anatomy to physiology , 2014, International journal of dermatology.

[100]  Pietro Liò,et al.  Forensic DNA and bioinformatics , 2006, Briefings Bioinform..

[101]  M. Holland,et al.  Mitochondrial DNA Sequence Analysis - Validation and Use for Forensic Casework. , 1999, Forensic science review.