An enhanced MITOMAP with a global mtDNA mutational phylogeny

By E. Ruiz‐Pesini, M. Lott, Vincent Procaccio, Jason C. Poole, Marty C. Brandon, D. Mishmar, Christina Yi, James Kreuziger, Pierre Baldi, Douglas C. Wallace. Nucleic Acids Res., 2006

621 citations recorded by the source corpus.

The MITOMAP () data system for the human mitochondrial genome has been greatly enhanced by the addition of a navigable mutational mitochondrial DNA (mtDNA) phylogenetic tree of ∼3000 mtDNA coding region sequences plus expanded pathogenic mutation tables and a nuclear-mtDNA pseudogene (NUMT) data base. The phylogeny reconstructs the entire mutational history of the human mtDNA, thus defining the mtDNA haplogroups and differentiating ancient from recent mtDNA mutations. Pathogenic mutations are classified by both genotype and phenotype, and the NUMT sequences permits detection of spurious inclusion of pseudogene variants during mutation analysis. These additions position MITOMAP for the implementation of our automated mtDNA sequence analysis system, Mitomaster.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3b6b243c2be74473085592757c624012edbfa141

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Citations in the corpus

Mitochondrial DNA: more than an evolutionary bystander (2014, background): “Extensive and ongoing research has shown that mtDNA mutations can profoundly affect mitochondrial function (Ruiz-Pesini et al. 2007).”
The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution (2012, methodology): “The latter are well covered by MIT-OMAP (Ruiz-Pesini et al., 2007 pathological mutations; a link to MITOMAP is provided in HGMD. Mutation data in HGMD are accessible on the basis of every gene being allocated one Web page per mutation type, if data of that type are present.”
Mitochondrial Energetics and Therapeutics (2010, positive): “MnSOD: manganese superoxide dismutase (Sod2) been published, approximately one-third are located in mtDNA-encoded polypeptide genes (3, 87).”
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets (2012, background): “Reads mapping against the mitochondrial genome were extracted from the hg18-mapped BAM ﬁles and strin-gently remapped (BWA unique) against the Cambridge reference (37) to allow for easy comparison with Mitomap entries.”
The Human Gene Mutation Database: 2008 update (2009, neutral): “These are well covered by COSMIC [2] and MITOMAP [3], respectively.”
The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine (2013, neutral): “HGMD does not include either somatic or mitochondrial mutations, which are well covered by COSMIC (Forbes et al. 2011) and MitoMap (Ruiz-Pesini et al. 2007), respectively.”
Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation (2009, background): “Recently, a global mtDNA phylogeny based on 2959 coding region sequences was published as part of the MITOMAP database (Ruiz-Pesini et al., 2007).”