MitoSAVE: Mitochondrial sequence analysis of variants in Excel

Forensic Science International: Genetics

Volumn 12, Issue , 2014, Pages 122-125

  King, Jonathan L ^a   Sajantila, Antti ^a,b   Budowle, Bruce ^a,c  

^a UNIVERSITY OF NORTH TEXAS HEALTH SCIENCE CENTER   (United States)

^b UNIVERSITY OF HELSINKI   (Finland)

^c KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Bioinformatics; Forensic nomenclature; Massively Parallel Sequencing (MPS); Mitochondrial genome (mtGenome); Mitochondrial haplotype; Variant Call Format (VCF) file

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA; SPACER DNA; TRANSFER RNA;

ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; DINUCLEOTIDE REPEAT; GENE SEQUENCE; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; INDEL MUTATION; MITOCHONDRIAL GENOME; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

GENOME, MITOCHONDRIAL; HAPLOTYPES; HUMANS; SOFTWARE;

EID: 84903214880     PISSN: 18724973     EISSN: 18780326     Source Type: Journal    
DOI: 10.1016/j.fsigen.2014.05.013     Document Type: Article

References (39)

1. J. Nunnari, and A. Suomalainen Mitochondria: in sickness and in health Cell 148 2012 1145 1159
2. D.C. Wallace, and D. Chalkia Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease Cold Spring Harbor Persp. Biol. 5 2013 a021220
3. S. Bannwarth, V. Procaccio, A.S. Lebre, C. Jardel, A. Chaussenot, and C. Hoarau et al. Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders J. Med. Genet. 50 2013 704 714
4. M. van Oven, and M. Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation Hum. Mutat. 30 2009 E386 E394
5. S.L. Mitchell, R. Goodloe, K. Brown-Gentry, S.A. Pendergrass, D.G. Murdock, and D.C. Crawford Characterization of mitochondrial haplogroups in a large population-based sample from the United States Hum. Genet. 2014 1 8
6. T. Kivisild, M. Reidla, E. Metspalu, A. Rosa, A. Brehm, and E. Pennarun et al. Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears Am. J. Hum. Genet. 75 2004 752 770
7. M. Richards, V. Macaulay, A. Torroni, and H.-J. Bandelt In search of geographical patterns in European mitochondrial DNA Am. J. Hum. Genet. 71 2002 1168 1174
8. M.R. Wilson, J.A. DiZinno, D. Polanskey, J. Replogle, and B. Budowle Validation of mitochondrial DNA sequencing for forensic casework analysis Int. J. Leg. Med. 108 1995 68 74
9. M.M. Holland, and T.J. Parsons Mitochondrial DNA sequence analysis-validation and use for forensic casework Forensic Sci. Rev. 11 1999 21 50
10. N. Howell, J.L. Elson, C. Howell, and D.M. Turnbull Relative rates of evolution in the coding and control regions of African mtDNAs Mol. Biol. Evol. 24 2007 2213 2221
11. E.A. Lyons, M.K. Scheible, K. Sturk-Andreaggi, J.A. Irwin, and R.S. Just A high-throughput Sanger strategy for human mitochondrial genome sequencing BMC Genomics 14 2013 881
12. L. Fendt, B. Zimmermann, M. Daniaux, and W. Parson Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences BMC Genomics 10 2009 139
13. M. Coble, R. Just, J. O'Callaghan, I. Letmanyi, C. Peterson, and J. Irwin et al. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians Int. J. Leg. Med. 118 2004 137 146
14. S. Sigurdsson, M. Hedman, P. Sistonen, A. Sajantila, and A.-C. Syvänen A microarray system for genotyping 150 single nucleotide polymorphisms in the coding region of human mitochondrial DNA Genomics 87 2006 534 542
15. A. Brandstätter, T.J. Parsons, and W. Parson Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups Int. J. Leg. Med. 117 2003 291 298
16. Scientific Working Group on DNA Analysis Methods (SWGDAM) Interpretation Guidelines for Mitochondrial DNA Analysis by Forensic DNA Testing Laboratories 2013 http://swgdam.org/SWGDAM%20mtDNA-Interpretation-Guidelines-APPROVED-073013. pdf
17. M.R. Wilson, M.W. Allard, K. Monson, K.W.P. Miller, and B. Budowle Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region Forensic Sci. Int. 129 2002 35 42
18. B. Budowle, D. Polanskey, C.L. Fisher, B.K. Den Hartog, R.B. Kepler, and J.W. Elling Automated alignment and nomenclature for consistent treatment of polymorphisms in the human mitochondrial DNA control region J. Forensic Sci. 55 2010 1190 1195
19. G. Tully, W. Bär, B. Brinkmann, A. Carracedo, P. Gill, and N. Morling et al. Considerations by the European DNA profiling (EDNAP) group on the working practices, nomenclature and interpretation of mitochondrial DNA profiles Forensic Sci. Int. 124 2001 83 91
20. H.-J. Bandelt, and W. Parson Consistent treatment of length variants in the human mtDNA control region: a reappraisal Int. J. Leg. Med. 122 2008 11 21
21. S. Anderson, A.T. Bankier, B.G. Barrell, M.H.L. de Bruijn, A.R. Coulson, and J. Drouin et al. Sequence and organization of the human mitochondrial genome Nature 290 1981 457 465
22. R.M. Andrews, I. Kubacka, P.F. Chinnery, R.N. Lightowlers, D.M. Turnbull, and N. Howell Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA Nat. Genet. 23 1999 147
23. W. Parson, A. Brandstätter, A. Alonso, N. Brandt, B. Brinkmann, and A. Carracedo et al. The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives Forensic Sci. Int. 139 2004 215 226
24. W. Parson, and A. Dür EMPOP - a forensic mtDNA database Forensic Sci. Int. Genet. 1 2007 88 92
25. H.-J. Bandelt, P. Lahermo, M. Richards, and V. Macaulay Detecting errors in mtDNA data by phylogenetic analysis Int. J. Leg. Med. 115 2001 64 69
26. H.-J. Bandelt, M. van Oven, and A. Salas Haplogrouping mitochondrial DNA sequences in legal medicine/forensic genetics Int. J. Leg. Med. 126 2012 901 916
27. A.W. Röck, A. Dür, M. van Oven, and W. Parson Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA) Forensic Sci. Int. Genet. 2013
28. A. Kloss-Brandstätter, D. Pacher, S. Schönherr, H. Weissensteiner, R. Binna, and G. Specht et al. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups Hum. Mutat. 32 2011 25 32
29. D. Vianello, F. Sevini, G. Castellani, L. Laura, CapriF M., and FranceschiF C. HAPLOFIND. A new method for high-throughput mtDNA Haplogroup assignment Hum. Mutat. 2013
30. W. Parson, C. Strobl, G. Huber, B. Zimmermann, S.M. Gomes, and L. Souto et al. Evaluation of next generation mtGenome sequencing using the ion torrent personal genome machine (PGM) Forensic Sci. Int. Genet. 7 2013 543 549
31. J.E. Templeton, P.M. Brotherton, B. Llamas, J. Soubrier, W. Haak, and A. Cooper et al. DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification Investig. Genet. 4 2013
32. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
33. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, and A. Kernytsky et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res. 20 2010 1297 1303
34. P. Danecek, A. Auton, G. Abecasis, C.A. Albers, E. Banks, and M.A. DePristo et al. The Variant Call Format and VCFtools Bioinformatics 27 2011 2156 2158
35. J.L. King, B.L. LaRue, N. Novroski, M. Stoljarova, S.B. Seo, and X. Zeng et al. High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq Forensic Sci. Int. Genet. 2014 10.1016/j.fsigen.2014.06.001 (In Press)
36. J.G. Lorenz, and D.G. Smith Distribution of the 9-bp mitochondrial DNA region V deletion among North American Indians Hum. Biol. 77 1994 7 8 8
37. W. Watkins, M. Bamshad, M. Dixon, B. Bhaskara Rao, J. Naidu, and P. Reddy et al. Multiple origins of the mtDNA 9-bp deletion in populations of South India Am. J. Phys. Anthropol. 109 1999 147 158
38. NCBI GenBank Database, http://www.ncbi.nlm.nih.gov/genbank/.
39. D.M. Behar, M. van Oven, S. Rosset, M. Metspalu, E.-L. Loogväli, and N.M. Silva et al. A Copernican reassessment of the human mitochondrial DNA tree from its root Am. J. Hum. Genet. 90 2012 675 684