- #Mitochondrial dna sequence analysis software#
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Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate and accuracy for the Affymetrix MitoChip v2.0 platform. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection.
Glebs A, Stencel E, Knoche K (2003) The “Go-to” choice: GoTaq DNA polymerase.Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Glebs A, Stencel E, Knoche K (2003) The “Go-to” choice: GoTaq DNA polymerase. van Oven M, Kayser M (2008) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Kloss-Brandstätter A, Pacher D, Schönherr S, Weissensteiner H, Binna R, Specht G et al (2011) HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. #Mitochondrial dna sequence analysis windows#
Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Fendt L, Zimmermann B, Daniaux M, Parson W (2009) Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences. Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA (2007) Whole-mtDNA genome sequence analysis of ancient African lineages. Coble MD, Just RS, O'Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA et al (2004) Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Levin BC, Holland KA, Hancock DK, Coble M, Parsons TJ, Kienker LJ et al (2003) Comparison of the complete mtDNA genome sequences of human cell lines - HL-60 and GM 10742A - from individuals with pro-myelocytic leukemia and leber hereditary optic neuropathy, respectively, and the inclusion of HL-60 in the NIST human mitochondrial DNA standard reference material - SRM 2392-I. Taylor RW, Taylor GA, Durham SE, Turnbull DM (2001) The determination of complete human mitochondrial DNA sequences in single cells: implications for the study of somatic mitochondrial DNA point mutations. Rieder MJ, Taylor SL, Tobe VO, Nickerson DA (1998) Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. 
#Mitochondrial dna sequence analysis torrent#
Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L et al (2013) Evaluation of next generation mtGenome sequencing using the Ion Torrent personal genome machine (PGM). Bandelt HJ, Salas A (2012) Current next generation sequencing technology may not meet forensic standards. Sullivan KM, Hopgood R, Gill P (1992) Identification of human remains by amplification and automated sequencing of mitochondrial DNA. Sullivan KM, Hopgood R, Lang B, Gill P (1991) Automated amplification and sequencing of human mitochondrial DNA. Higuchi R, von Beroldingen CH, Sensabaugh GF, Erlich HA (1988) DNA typing from single hairs.
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