Abstract
The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly
publishes guidelines and recommendations concerning the application of DNA polymorphisms
to the question of human identification. Previous recommendations published in 2000
addressed the analysis and interpretation of mitochondrial DNA (mtDNA) in forensic
casework. While the foundations set forth in the earlier recommendations still apply,
new approaches to the quality control, alignment and nomenclature of mitochondrial
sequences, as well as the establishment of mtDNA reference population databases, have
been developed. Here, we describe these developments and discuss their application
to both mtDNA casework and mtDNA reference population databasing applications. While
the generation of mtDNA for forensic casework has always been guided by specific standards,
it is now well-established that data of the same quality are required for the mtDNA
reference population data used to assess the statistical weight of the evidence. As
a result, we introduce guidelines regarding sequence generation, as well as quality
control measures based on the known worldwide mtDNA phylogeny, that can be applied
to ensure the highest quality population data possible. For both casework and reference
population databasing applications, the alignment and nomenclature of haplotypes is
revised here and the phylogenetic alignment proffered as acceptable standard. In addition,
the interpretation of heteroplasmy in the forensic context is updated, and the utility
of alignment-free database searches for unbiased probability estimates is highlighted.
Finally, we discuss statistical issues and define minimal standards for mtDNA database
searches.
Keywords
To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:
Subscribe to Forensic Science International: GeneticsAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- Mitochondrial DNA sequence analysis – validation and use for forensic casework.Forensic Sci. Rev. 1999; 11: 21-50
- DNA commission of the International Society of Forensic Genetics: guidelines for mitochondrial DNA typing.Forensic Sci. Int. 2000; 110: 79-85
- Guidelines for mitochondrial DNA (mtDNA) Nucleotide sequence information.Forensic Sci. Commun. 2003; 5
- EMPOP – a forensic mtDNA database.Forensic Sci. Int. Genet. 2007; 1: 88-92
- Interpretation Guidelines for Mitochondrial DNA Analysis by Forensic DNA Testing Laboratories.2013: 1-23 (http://swgdam.org/SWGDAM%20mtDNA_Interpretation_Guidelines_APPROVED_073013.pdf)
- Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA.Nat. Genet. 1999; 23: 14
- The GEDNAP (German DNA Profiling Group) Proficiency Testing System.2013 (http://www.gednap.org)
- error prophylaxis: assessing the causes of errors in the GEP’02-03 proficiency testing trial.Forensic Sci. Int. 2005; 148: 191-198
- Analysis of body fluid mixtures by mtDNA sequencing: an inter-laboratory study of the GEP-ISFG working group.Forensic Sci. Int. 2007; 168: 42-56
- The GHEP-EMPOP collaboration on mtDNA population data – a new resource for forensic casework.Forensic Sci. Int. Genet. 2011; 5: 146-151
- GHEP-ISFG proficiency test 2011: paper challenge on evaluation of mitochondrial DNA results.Forensic Sci. Int. Genet. 2013; 7: 10-15
- Federal Bureau of Investigation Quality Assurance Standards for Forensic DNA Testing Laboratories.2011
- Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software.Croat. Med. J. 2014; 55: 115-120
- The fingerprint of phantom mutations in mitochondrial DNA data.Am. J. Hum. Genet. 2002; 71: 1150-1160
- Phantom mutation hotspots in human mitochondrial DNA.Electrophoresis. 2005; 26: 3414-3429
- Artificial recombination in forensic mtDNA population databases.Int. J. Legal Med. 2004; 118: 267-273
- Extended guidelines for mtDNA typing of population data in forensic science.Forensic Sci. Int. Genet. 2007; 1: 13-19
- Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database.Int. J. Legal Med. 2004; 118: 294-306
- Application of a quasi-median network analysis for the visualization of character conflicts to a population sample of mitochondrial DNA control region sequences from southern Germany (Ulm).Int. J. Legal Med. 2006; 120: 310-314
- Development and expansion of high-quality control region databases to improve forensic mtDNA evidence interpretation.Forensic Sci. Int. Genet. 2007; 1: 154-157
- ‘Mitominis’: multiplex PCR analysis of reduced size amplicons for compound sequence analysis of the entire mtDNA control region in highly degraded samples.Int. J. Legal Med. 2008; 122: 385-388
- Mini-midi-mito: adapting the amplification and sequencing strategy of mtDNA to the degradation state of crime scene samples.Forensic Sci. Int. Genet. 2009; 3: 149-153
- Improved MtDNA sequence analysis of forensic remains using a mini-primer set amplification strategy.J. Forensic Sci. 2001; 46: 247-253
- Sequence and organization of the human mitochondrial genome.Nature. 1981; 290: 457-465
- A “Copernican” reassessment of the human mitochondrial DNA tree from its root.Am. J. Hum. Genet. 2012; 90: 675-684
- A cautionary note on switching mitochondrial DNA reference sequences in forensic genetics.Forensic Sci. Int. Genet. 2012; 6: e182-e184
- The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies.J. Hum. Genet. 2014; 59: 66-77
- Improving the reconstructed sapiens reference sequence of mitochondrial DNA.Forensic Sci. Int. Genet. 2013; 7: e74-e75
- Translating DNA data tables into quasi-median networks for parsimony analysis and error detection.Mol. Phylogenet. Evol. 2007; 42: 256-271
- Recommendations for consistent treatment of length variants in the human mtDNA control region.Forensic Sci. Int. 2002; 129: 35-42
- Automated alignment and nomenclature for consistent treatment of polymorphisms in the human mitochondrial DNA control region.J. Forensic Sci. 2010; 55: 1190-1195
- Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database.Int. J. Legal Med. 2010; 124: 263-268
- Consistent treatment of length variants in the human mtDNA control region: a reappraisal.Int. J. Legal Med. 2008; 122: 11-21
- Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation.Hum. Mutat. 2009; 30: E386-E394
- SAM: string-based sequence search algorithm for mitochondrial DNA database queries.Forensic Sci. Int. Genet. 2011; 5: 126-132
- The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age.Am. J. Hum. Genet. 2000; 66: 1384-1397
- Heteroplasmy in mtDNA and the weight of evidence in forensic mtDNA analysis: a case report.Int. J. Legal Med. 2001; 114: 186-190
- Mitochondrial DNA Heteroplasmy.Forensic Sci. Rev. 2004; 16: 2-19
- Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts.Forensic Sci. Int. 2004; 140: 1-11
- Recurrent tissue-specific mtDNA mutations are common in humans.PLoS Genet. 2013; 9: e1003929
- Human brain contains high levels of heteroplasmy in the noncoding regions of mitochondrial DNA.Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 12382-12387
- Investigation of point heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from over 5000 global population samples.J. Mol. Evol. 2009; 68: 516-527
- Forensic mitochondrial DNA analysis of 691 casework hairs.J. Forensic Sci. 2005; 50: 73-80
- A high observed substitution rate in the human mitochondrial DNA control region.Nat. Genet. 1997; 15: 363-368
- Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy.Croat. Med. J. 2011; 52: 299-313
- Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II.Nat. Genet. 1996; 12: 417-420
- Population data for 101 Austrian Caucasian mitochondrial DNA d-loop sequences: application of mtDNA sequence analysis to a forensic case.Int. J. Legal Med. 1998; 111: 124-132
- Evaluating sequence-derived mtDNA length heteroplasmy by amplicon size analysis.Forensic Sci. Int. Genet. 2011; 5: 142-145
- Evaluating length heteroplasmy in the human mitochondrial DNA control region.Int. J. Legal Med. 2009; 124: 133-142
- A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics.Biochem. Biophys. Res. Commun. 2005; 335: 891-899
- The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives.Forensic Sci. Int. 2004; 139: 215-226
- Generating population data for the EMPOP database – an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example.Forensic Sci. Int. 2007; 166: 164-175
- Application of a west Eurasian-specific filter for quasi-median network analysis: sharpening the blade for mtDNA error detection.Forensic Sci. Int. Genet. 2011; 5: 133-137
- Publication of population data of linearly inherited DNA markers in the International Journal of Legal Medicine.Int. J. Legal Med. 2010; 124: 505-509
- Update of the guidelines for the publication of genetic population data.Forensic Sci. Int. Genet. 2014; 10: A1-A2
- Haplogrouping mitochondrial DNA sequences in Legal Medicine/Forensic Genetics.Int. J. Legal Med. 2012; 126: 901-916
- Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA).Forensic Sci. Int. Genet. 2013; 7: 601-609
- Phylogeographic investigations: the role of trees in forensic genetics.Forensic Sci. Int. 2007; 168: 1-13
- A melting pot of multicontinental mtDNA lineages in admixed Venezuelans.Am. J. Phys. Anthropol. 2012; 147: 78-87
- Indian signatures in the westernmost edge of the European Romani diaspora: new insight from mitogenomes.PLOS ONE. 2013; 8: e75397
- The use of confidence or fiducial limits illustrated in the case of the binomial.Biometrika. 1934; 26: 404-413
- DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands.Forensic Sci. Int. 1994; 64: 125-140
- Estimating haplotype frequency and coverage of databases.PLoS ONE. 2008; 3: e3988
- Inferring the most likely geographical origin of mtDNA sequence profiles.Ann. Hum. Genet. 2004; 68: 461-471
- Fundamental problem of forensic mathematics – the evidential value of a rare haplotype.Forensic Sci. Int. Genet. 2010; 4: 281-291
Article info
Publication history
Published online: July 28, 2014
Accepted:
July 19,
2014
Received:
July 15,
2014
Identification
Copyright
© 2014 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
