Research Article| Volume 26, P77-84, January 2017

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A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing

Published:October 24, 2016DOI:


      A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot™-based screening assay (denoted mini-mtSNaPshot) (Weiler et al., 2016) [1] that targets 18 single nucleotide polymorphism (SNP) positions in the mitochondrial (mt) DNA control region and allows for discrimination of major European mtDNA haplogroups. Besides the organising laboratory, 14 forensic genetics laboratories were involved in the analysis of 13 samples, which were centrally prepared and thoroughly tested prior to shipment. The samples had a variable complexity and comprised straightforward single-source samples, samples with dropout or altered peak sizing, a point heteroplasmy and two-component mixtures resulting in one to five bi-allelic calls. The overall success rate in obtaining useful results was high (97.6%) given that some of the participating laboratories had no previous experience with the typing technology and/or mtDNA analysis. The majority of the participants proceeded to haplotype inference to assess the feasibility of assigning a haplogroup and checking phylogenetic consistency when only 18 SNPs are typed. To mimic casework procedures, the participants compared the SNP typing data of all 13 samples to a set of eight mtDNA reference profiles that were described according to standard nomenclature (Parson et al., 2014) [2], and indicated whether these references matched each sample or not. Incorrect scorings were obtained for 2% of the comparisons and derived from a subset of the participants, indicating a need for training and guidelines regarding mini-mtSNaPshot data interpretation.


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        • Weiler N.E.C.
        • de Vries G.
        • Sijen T.
        Development of a control region-based mtDNA SNaPshot selection tool, integrated into a mini amplicon sequencing method.
        Sci. Justice. 2016; 56: 96-103
        • Parson W.
        • Gusmao L.
        • Hares D.R.
        • Irwin J.A.
        • Mayr W.R.
        • Morling N.
        • Pokorak E.
        • Prinz M.
        • Salas A.
        • Schneider P.M.
        • Parsons T.J.
        DNA Commission of the International Society for Forensic Genetics: revised and extended guidelines for mitochondrial DNA typing.
        Forensic Sci. Int. Genet. 2014; 13: 134-142
        • Parson W.
        • Fendt L.
        • Ballard D.
        • Borsting C.
        • Brinkmann B.
        • Carracedo A.
        • Carvalho M.
        • Coble M.D.
        • Real F.C.
        • Desmyter S.
        • Dupuy B.M.
        • Harrison C.
        • Hohoff C.
        • Just R.
        • Kramer T.
        • Morling N.
        • Salas A.
        • Schmitter H.
        • Schneider P.M.
        • Sonntag M.L.
        • Vallone P.M.
        • Brandstatter A.
        Identification of West Eurasian mitochondrial haplogroups by mtDNA SNP screening: results of the 2006–2007 EDNAP collaborative exercise.
        Forensic Sci. Int. Genet. 2008; 2: 61-68
        • Kohnemann S.
        • Pfeiffer H.
        Application of mtDNA SNP analysis in forensic casework.
        Forensic Sci. Int. Genet. 2011; 5: 216-221
        • Parsons T.J.
        • Coble M.D.
        Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome.
        Croat. Med. J. 2001; 42: 304-309
        • Aquadro C.F.
        • Greenberg B.D.
        Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals.
        Genetics. 1983; 103: 287-312
        • Melton T.
        • Wilson M.
        • Batzer M.
        • Stoneking M.
        Extent of heterogeneity in mitochondrial DNA of European populations.
        J. Forensic Sci. 1997; 42: 437-446
        • Piercy R.
        • Sullivan K.M.
        • Benson N.
        • Gill P.
        The application of mitochondrial DNA typing to the study of white Caucasian genetic identification.
        Int. J. Legal Med. 1993; 106: 85-90
        • Stoneking M.
        • Hedgecock D.
        • Higuchi R.G.
        • Vigilant L.
        • Erlich H.A.
        Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes.
        Am. J. Hum. Genet. 1991; 48: 370-382
        • Anderson E.C.
        • Garza J.C.
        The power of single-nucleotide polymorphisms for large-scale parentage inference.
        Genetics. 2006; 172: 2567-2582
        • Just R.S.
        • Leney M.D.
        • Barritt S.M.
        • Los C.W.
        • Smith B.C.
        • Holland T.D.
        • Parsons T.J.
        The use of mitochondrial DNA single nucleotide polymorphisms to assist in the resolution of three challenging forensic cases.
        J. Forensic Sci. 2009; 54: 887-891
        • Salas A.
        • Quintans B.
        • Alvarez-Iglesias V.
        SNaPshot typing of mitochondrial DNA coding region variants.
        Methods Mol. Biol. 2005; 297: 197-208
        • Eichmann C.
        • Parson W.
        ‘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
        • Andrews R.M.
        • Kubacka I.
        • Chinnery P.F.
        • Lightowlers R.N.
        • Turnbull D.M.
        • Howell N.
        Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA.
        Nat. Genet. 1999; : 147
        • Just R.S.
        • Irwin J.A.
        • Parson W.
        Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing.
        Forensic Sci. Int. Genet. 2015; 18: 131-139
        • Irwin J.A.
        • Saunier J.L.
        • Niederstatter H.
        • Strouss K.M.
        • Sturk K.A.
        • Diegoli T.M.
        • Brandstatter A.
        • Parson W.
        • Parsons T.J.
        Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples.
        J. Mol. Evol. 2009; 68: 516-527
        • Kloss-Brandstatter A.
        • Pacher D.
        • Schonherr S.
        • Weissensteiner H.
        • Binna R.
        • Specht G.
        • Kronenberg F.
        HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups.
        Hum. Mutat. 2011; 32: 25-32
        • van Oven M.
        • Kayser M.
        Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation.
        Hum. Mutat. 2009; 30: E386-E394
        • Fan L.
        • Yao Y.G.
        MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations.
        Mitochondrion. 2011; 11: 351-356
        • Fan L.
        • Yao Y.G.
        An update to MitoTool: using a new scoring system for faster mtDNA haplogroup determination.
        Mitochondrion. 2013; 13: 360-363
        • Rubino F.
        • Piredda R.
        • Calabrese F.M.
        • Simone D.
        • Lang M.
        • Calabrese C.
        • Petruzzella V.
        • Tommaseo-Ponzetta M.
        • Gasparre G.
        • Attimonelli M.
        HmtDB, a genomic resource for mitochondrion-based human variability studies.
        Nucleic Acids Res. 2012; 40: D1150-D1159
        • Parson W.
        • Dur A.
        EMPOP-a forensic mtDNA database.
        Forensic Sci. Int. Genet. 2007; 1: 88-92
        • Röck A.W.
        • Dür A.
        • van Oven M.
        • Parson W.
        Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA).
        Forensic Sci. Int. Genet. 2013; 7: 601-609
        • Bandelt H.J.
        • van Oven M.
        • Salas A.
        Haplogrouping mitochondrial DNA sequences in legal medicine/forensic genetics.
        Int. J. Legal Med. 2012; 126: 901-916