mtDNA Variation and Analysis Using Mitomap and Mitomaster

Marie T. Lott1, Jeremy N. Leipzig2, Olga Derbeneva1, H. Michael Xie2, Dimitra Chalkia1, Mahdi Sarmady2, Vincent Procaccio3, Douglas C. Wallace4

1 Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, 2 Center for Biomedical Informatics, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, 3 Biochemistry and Genetics Department, Angers Hospital; UMR CNRS 6214/INSERM U1083, Angers, 4 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.23
DOI:  10.1002/0471250953.bi0123s44
Online Posting Date:  December, 2013
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Abstract

The Mitomap database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians, and genetic counselors for the past 25 years. The Mitomap protocol shows how users may look up human mitochondrial gene loci, search for public mitochondrial sequences, and browse or search for reported general population nucleotide variants as well as those reported in clinical disease. Within Mitomap is the powerful sequence analysis tool for human mitochondrial DNA, Mitomaster. The Mitomaster protocol gives step‐by‐step instructions showing how to submit sequences to identify nucleotide variants relative to the rCRS, determine the haplogroup, and view species conservation. User‐supplied sequences, GenBank identifiers, and single‐nucleotide variants may be analyzed. Curr. Protoc. Bioinform. 44:1.23.1‐1.23.26. © 2013 by John Wiley & Sons, Inc.

Keywords: biological database; information retrieval; human mitochondrial DNA; haplogroups; species conservation; GenBank sequences; single nucleotide variants

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Exploring mtDNA Variants with Mitomap
  • Basic Protocol 2: Analyzing mtDNA Variants with Mitomaster
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

  Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J., Staden, R., and Young, I.G. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457‐465.
  Andrews, R.M., Kubacka, I., Chinnery, P.F., Lightowlers, R.N., Turnbull, D.M., and Howell, N. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23:147.
  Kloss‐Brandstatter, A., Pacher, D., Schonherr, S., Weissensteiner, H., Binna, R., Specht, G., and Kronenberg, F. 2011. HaploGrep: A fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum. Mutat. 32:25‐32.
  van Oven, M. and Kayser, M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. (Online) 30:E386‐E394.
  Wallace, D.C., Lott, M.T., Brown, M.D., Huoponen, K., and Torroni, A. 1995. Report of the committee on human mitochondrial DNA. In Human Gene Mapping 1994, a Compendium (A.J. Cuticchia ed.) pp. 910‐954. The Johns Hopkins University Press, Baltimore, Md.
  Yao, Y.G., Salas, A., Logan, I., and Bandelt, H.J. 2009. mtDNA data mining in GenBank needs surveying. Am. J. Hum. Genet. 85:929‐933.
Key References
  Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C.J., Osborne, B.I., Pocock, M.R., Schattner, P., Senger, M., Stein, L.D., Stupka, E., Wilkinson, M.D. and Birney, E. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12:1611‐1618.
  Supporting publication for Bioperl.
  Steinbiss, S., Gremme, G., Scharfer, C., Mader, M., and Kurtz, S. 2009. AnnotationSketch: A genome annotation drawing library. Bioinformatics 25:533‐534.
  Supporting publication for AnnotationSketch
  Zaragoza, M.V., Brandon, M.C., Diegoli, M., Arbustini, E. and Wallace, D.C. 2011. Mitochondrial cardiomyopathies: How to identify candidate pathogenic mutations by mitochondrial DNA sequencing, MITOMASTER and phylogeny. Eur. J. Hum. Genet. 19:200‐207.
  Yao et al., 2009. See above.
Internet Resources
  http://www.mitomap.org
  Mitomap.
  http://mitomaster.mitomap.org
  Mitomaster.
  http://www.phylotree.org
  Phylotree.
  http://haplogrep.uibk.ac.at/
  Haplogrep.
  http://www.ncbi.nlm.nih.gov
  NCBI.
  http://blast.ncbi.nlm.nih.gov/
  BLAST.
  http://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1
  The rCRS: Homo sapiens mitochondrion, complete genome.
  http://www.bioinformatics.nl/tools/crab_fasta.html
  FASTA format.
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