mtGenome reference population databases and the future of forensic mtDNA analysis

Forensic Science International: Genetics

Volumn 5, Issue 3, 2011, Pages 222-225

  Irwin, Jodi A ^a   Parson, Walther ^b   Coble, Michael D ^a,c   Just, Rebecca S ^a  

^a ARMED FORCES INSTITUTE OF PATHOLOGY   (United States)

^b INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^c NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

Coding region; Database; Mitochondrial DNA

Indexed keywords

AMPLICON; ARTICLE; DNA DETERMINATION; DNA FINGERPRINTING; DNA SEQUENCE; FORENSIC GENETICS; GENE SEQUENCE; GENETIC CODE; HAPLOTYPE; HUMAN; LABORATORY; MASS SPECTROMETRY; MITOCHONDRIAL GENE; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; REFERENCE DATABASE; SINGLE NUCLEOTIDE POLYMORPHISM;

DATABASES, GENETIC; DNA, MITOCHONDRIAL; FORENSIC GENETICS; GENOME, HUMAN; HUMANS;

EID: 79953867044     PISSN: 18724973     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fsigen.2010.02.008     Document Type: Article

References (49)

1. M.M. Holland, D.L. Fisher, L.G. Mitchell, W.C. Rodriquez, J.J. Canik, C.R. Merril, et al., Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the Vietnam War, J. Forensic Sci. 38 (1993) 542-553. (Pubitemid 23152892)
2. J.M. Butler, B.C. Levin, Forensic applications of mitochondrial DNA, Trends Biotechnol. 16 (1998) 158-162. (Pubitemid 28172664)
3. M.M. Holland, T.J. Parsons, Mitochondrial DNA sequence analysis - validation and use for forensic casework, Forensic Sci. Rev. 11 (1999) 21-50.
4. A. Carracedo, W. Bar, P. Lincoln, W. Mayr, N. Morling, B. Olaisen, et al., DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing, Forensic Sci. Int. 110 (2000) 79-85.
5. T. Melton, K. Nelson, Forensic mitochondrial DNA analysis: two years of commercial casework experience in the United States, Croatian Med. J. 42 (2001) 298-303. (Pubitemid 32606996)
6. S. Lutz, H.-J. Weisser, J. Heizmann, S. Pollak, Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany, Int. J. Legal Med. 111 (1998) 67-77.
7. S. Lutz, H. Wittig, H.-J. Weisser, J. Heizmann, A. Junge, N. Dimo-Simonin, 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? Forensic Sci. Int. 113 (2000) 97-101. (Pubitemid 30649719)
8. A. Brandstätter, H. Niederstätter, M. Pavlic, P. Grubwieser, W. Parson, 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. 166 (2007) 164-175.
9. S.D. Lee, Y.S. Lee, J.B. Lee, Polymorphism in the mitochondrial cytochrome B gene in Koreans. An additional marker for individual identification, Int. J. Legal Med. 116 (2002) 74-78. (Pubitemid 36056579)
10. H. Andreasson, A. Asp, A. Alderborn, U. Gyllensten, M. Allen, Mitochondrial sequence analysis for forensic identification using pyrosequencing technology, BioTechniques 32 (2002) 124-133. (Pubitemid 34052759)
11. S. Lutz-Bonengel, U. Schmidt, T. Schmitt, S. Pollak, Sequence polymorphisms within the human mitochondrial genes MTATP6, MTATP8, and MTND4, Int. J. Legal Med. 117 (2003) 133-142. (Pubitemid 36781807)
12. M.D. Coble, R.S. Just, J.E. O'Callaghan, I.H. Letmanyi, C.T. Peterson, J.A. Irwin, et al., Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians, Int. J. Legal Med. 118 (2004) 137-146.
13. B. Quintáns, V. Álvarez-Iglesias, A. Salas, C. Phillips, M.V. Lareu, A. Carracedo, Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing, Forensic Sci. Int. 140 (2004) 251-257.
14. K.A. Sturk, M.D. Coble, S.M. Barritt, T.J. Parsons, R.S. Just, The application of mtDNA SNPs to a forensic case, Forensic Sci. Int. Genet. Supplement Series 1 (2008) 295-297.
15. R.S. Just, M.D. Leney, S.M. Barritt, C.W. Los, B.C. Smith, T.D. Holland, et al., The Use of mitochondrial DNA single nucleotide polymorphisms to assist in the resolution of three challenging forensic cases, J. Forensic Sci. 54 (2009) 887-891.
16. J.A. Irwin, S.M. Edson, O. Loreille, R.S. Just, S.M. Barritt, D.A. Lee, et al., DNA identification of "Earthquake McGoon" 50 years postmortem, J. Forensic Sci. 52 (2007) 1115-1118.
17. A. Brandstätter, T.J. Parsons, W. Parson, Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups, Int. J. Legal Med. 117 (2003) 291-298.
18. W. Parson, A. Brandstätter, H. Niederstätter, P. Grubwieser, R. Scheithauer, Unraveling the mystery of Nanga Parbat, Int. J. Legal Med. 121 (2007) 309-310.
19. V. Álvarez-Iglesias, J.C. Jaime, Á. Carracedo, A. Salas, Coding region mitochondrial coding region SNPs: Targeting East Asian and Native American haplogroups, Forensic Sci. Int. Genet. 1 (2007) 44-55. (Pubitemid 46705220)
20. T.M. Nelson, R.S. Just, O. Loreille, M.S. Schanfield, D. Podini, Development of a multiplex single base extension assay for mitochondrial DNA haplogroup typing, Croatian Med. J. 48 (2007) 460-472. (Pubitemid 47330046)
21. S. Köhnemann, H. Pfeiffer, Application of mtDNA SNP analysis in forensic casework, Forensic Sci. Int. Genet. 5 (2011) 216-221.
22. R.S. Just, O.M. Loreille, J.E. Molto, D.A. Merriwether, S.R. Woodward, C. Matheson, et al., Titanic's unknown child: the critical role of the mitochondrial DNA coding region in a re-identification effort, Forensic Sci. Int. Genet. 5 (2011) 231-235.
23. M. Allen, H. Andreasson, Mitochondrial d-loop and coding sequence analysis using pyrosequencing, Methods Mol. Biol. 297 (2004) 179-196.
24. P.M. Vallone, R.S. Just, M.D. Coble, J.M. Butler, T.J. Parsons, A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome, Int. J. Legal Med. 118 (2004) 147-157.
25. A. Salas, B. Quintáns, V. Álvarez-Iglesias, SNaPshot typing of mitochondrial DNA coding region variants, in: A. Carracedo (Ed.), Forensic DNA Typing Protocols, Methods in Molecular Biology, Humana Press, Totowa, New Jersey, 2005, pp. 197-208.
26. P.M. Vallone, J.P. Jakupciak, M.D. Coble, Forensic application of the Affymetrix human mitochondrial resequencing array, Forensic Sci. Int. Genet. 1 (2007) 196-198. (Pubitemid 46760399)
27. R.S. Just, A.M. Lehrmann, K.E. Harris, M.D. Coble, Comparison of the AB mitoSEQr resequencing sets to standard mtDNA sequencing protocols, in: Presented at the English Speaking Working Group Meeting of the International Society for Forensic Genetics, Sinaia, Romania, 2008.
28. C. Calloway, S. Stuart, H. Erlich, Development of a multiplex PCR and linear array probe assay targeting informative polymorphisms within the entire mitochondrial genome, 2009. http://www.ncjrs.gov/pdffiles1/nij/grants/228279. pdf.
29. T.A. Hall, B. Budowle, Y. Jiang, L. Blyn, M. Eshoo, K. Sannes-Lowery, et al., Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: a novel tool for the identification and differentiation of humans, Anal. Biochem. 344 (2005) 53-69.
30. H. Oberacher, H. Niederstätter, F. Pitterl, W. Parson, Profiling 627 mitochondrial nucleotides via the analysis of a 23-plex polymerase chain reaction by liquid chromatography-electrospray ionization time-of-flight mass spectrometry, Anal. Chem. 78 (2006) 7816-7827.
31. T.A. Hall, K.A. Sannes-Lowery, L.D. McCurdy, C. Fisher, T. Anderson, A. Henthorne, et al., Base composition profiling of human mitochondrial DNA using polymerase chain reaction and direct automated electrospray ionization mass spectrometry, Anal. Chem. 81 (2009) 7515-7526.
32. M. Cerezo, V. Černý, A. Carracedo, A. Salas, Applications of MALDI-TOF MS to largescale human mtDNA population-based studies, Electrophoresis 30 (2009) 3665-3673.
33. E.I. Rogaev, A.P. Grigorenko, G. Faskhutdinova, E.L.W. Kittler, Y.K. Moliaka, Genotype analysis identifies the cause of the "royal disease", Science 326 (2009) 817.
34. B. Brenig, J. Beck, E. Schütz, Shotgun metagenomics of biological stains using ultra-deep DNA sequencing, Forensic Sci. Int. Genet., (2009), doi:10.1016/j.fsigen.2009.10.001.
35. J. Krause, A.W. Briggs, M. Kircher, T. Maricic, N. Zwyns, A. Derevianko, et al., A complete mtDNA genome of an early modern human from Kostenki, Russia, Curr. Biol. 20 (2010) 231-236.
36. Y.-G. Yao, A. Salas, I. Logan, H.-J. Bandelt, MtDNA data mining in GenBank needs surveying, Am. J. Hum. Genet. 85 (2009) 929-933.
37. Y.S. Lee, W.Y. Kim, M. Ji, J.H. Kim, J. Bhak, MitoVariome: a variome database of human mitochondrial DNA, BMC Genomics (2009) S12.
38. H.-J. Bandelt, W. Parson, Consistent treatment of length variants in the human mtDNA control region: a reappraisal, Int. J. Legal Med. 122 (2008) 11-12.
39. W. Parson, A. Dür, EMOP - a forensic mtDNA database, Forensic Sci. Int. Genet. 1 (2007) 88-92.
40. W. Parson, H.-J. Bandelt, Extended guidelines for mtDNA typing of population data in forensic science, Forensic Sci. Int. Genet. 1 (2007) 13-17.
41. J. Irwin, J. Saunier, K. Strouss, K. Sturk, T. Diegoli, R. Just, M. Coble, W. Parson, T. Parsons, Development and expansion of high quality control region databases to improve forensic mtDNA evidence interpretation, Forensic Sci. Int. Genet. 1 (2007) 154-157.
42. A. Carracedo, J.M. Butler, L. Gusmão, W. Parson, L. Roewer, P.M. Schneider, Publication of population data for forensic purposes, Forensic Sci. Int. Genet. 4 (2010) 145-147.
43. M.D. Coble, P.M. Vallone, R.S. Just, T.M. Diegoli, B.C. Smith, T.J. Parsons, Effective strategies for forensic analysis in the mitochondrial DNA coding region, Int. J. Legal Med. 120 (2006) 27-32.
44. MITOMAP: A human mitochondrial genome database. http://www.mitomap.org, 2009.
45. H.-J. Bandelt, A. Salas, C.M. Bravi, What is a 'novel' mtDNA mutation-and does 'novelty' really matter? J. Hum. Genet. 51 (2006) 1073-1082.
46. H.-J. Bandelt, Y.-G. Yao, A. Salas, The search of 'novel' mtDNA mutations in hypertrophic cardiomyopathy: MITOMAPping as a risk factor, Int. J. Cardiol. 126 (2008) 439-442.
47. H.-J. Bandelt, A. Salas, R.W. Taylor, Y.-G. Yao, Exaggerated status of "novel" and "pathogenic" mtDNA sequence variants due to inadequate database searches, Hum. Mutat. 30 (2009) 191-196.
48. B. Budowle, U. Gyllensten, R. Chakraborty, M. Allen, Forensic analysis of the mitochondrial coding region and association to disease, Int. J. Legal Med. 119 (2005) 314-315.
49. L. Fendt, B. Zimmermann, M. Daniaux, W. Parson, Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences, BMC Genomics 10 (2009) 139.