77d8e74cbe26eadaf46c1ca3230f4d0bc59977cc gperez2 Mon Mar 3 14:18:27 2025 -0800 Adding chromosomes chrM,chrMT trackDb setting and note about MITOMAP data is available for chrM on hg38 and chrMT on hg19, refs #24849 diff --git src/hg/makeDb/trackDb/human/mitoMap.html src/hg/makeDb/trackDb/human/mitoMap.html index f38e8aa9d7e..a249b69b8f9 100644 --- src/hg/makeDb/trackDb/human/mitoMap.html +++ src/hg/makeDb/trackDb/human/mitoMap.html @@ -1,165 +1,172 @@

Description

NOTE: MITOMAP data is available for + chrM on hg38 and chrMT on hg19.
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This track shows annotations from MITOMAP. MITOMAP is a database of human mitochondrial DNA (mtDNA) information containing a compilation of mtDNA variation. It allows users to 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.

The data in these tracks are automatically updated from MitoMap weekly.

Display Conventions and Configuration

These data are separated into two tracks:

MITOMAP Control and Coding Variants

This data track contains variants, including mini insertions and deletions, in the complete mtDNA. The item colors correspond to the variant type: control region vs. coding region.

MITOMAP Disease Mutations

This data track contains disease-annotated mutations (variants) in the complete mtDNA. The item colors correspond to the variant type: coding/control vs. rRNA/tRNA.

For both tracks, item names correspond to the variant nucleotide change, and mousing over features displays all available metadata for MITOMAP. Linkouts to the specific MITOMAP datasets are available from the item description pages, however, you must input the variant on MITOMAP.

Abbreviations and Definitions

FL: Full-length sequences
CR: Control region sequences

Nucleotide changes are indicated as L-strand substitutions.

MT-NC: Non-coding locus
syn: Synonymous mutation

Variant Classification:

B: Benign
LB: Likely Benign
VUS: Variant of Uncertain Significance
LP: Likely Pathogenic
P: Pathogenic

Disease Associations:

LHON: Leber Hereditary Optic Neuropathy
MM: Mitochondrial Myopathy
AD: Alzheimer's Disease
LIMM: Lethal Infantile Mitochondrial Myopathy
ADPD: Alzheimer's Disease and Parkinson's Disease
MMC: Maternal Myopathy and Cardiomyopathy
NARP: Neurogenic muscle weakness, Ataxia, and Retinitis Pigmentosa (alternate phenotype: Leigh Disease)
FICP: Fatal Infantile Cardiomyopathy Plus, a MELAS-associated cardiomyopathy
MELAS: Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like episodes
LDYT: Leber's Hereditary Optic Neuropathy and Dystonia
MERRF: Myoclonic Epilepsy and Ragged Red Muscle Fibers
MHCM: Maternally Inherited Hypertrophic Cardiomyopathy
CPEO: Chronic Progressive External Ophthalmoplegia
KSS: Kearns-Sayre Syndrome
DM: Diabetes Mellitus
DMDF: Diabetes Mellitus with Deafness
CIPO: Chronic Intestinal Pseudoobstruction with Myopathy and Ophthalmoplegia
DEAF: Maternally Inherited Deafness or Aminoglycoside-Induced Deafness
PEM: Progressive Encephalopathy
SNHL: Sensorineural Hearing Loss

Mutation Terminology:

Homoplasmy: Pure mutant mtDNAs
Heteroplasmy: Mixture of mutant and normal mtDNAs
nd: Not determined

Mutation Status Definitions:

Reported: Indicates that one or more publications suggest the mutation may be pathogenic. This is not an assignment of pathogenicity by MITOMAP but is a report of literature. Previously, mutations with this status were termed "Prov" (provisional).
Cfrm (Confirmed): Indicates that at least two or more independent laboratories have published reports on the pathogenicity of a specific mutation. These mutations are generally accepted by the mitochondrial research community as being pathogenic. A status of "Cfrm" is not an assignment of pathogenicity by MITOMAP but is a report of published literature. Researchers and clinicians are cautioned that additional data and/or analysis may still be necessary to confirm the pathological significance of some of these mutations.
P.M. (Point Mutation/Polymorphism): Indicates that some published reports have determined the mutation to be a non-pathogenic polymorphism.

Methods

MITOMAP collected the sequences from GenBank, aligned them to the rCRS using BLASTn, and haplotyped them with Haplogrep via the Mitomaster web service.

The data were originally downloaded from the MITOMAP resource. For the Control and Coding Variants track, the following datasets were combined:

And for the Disease Mutations track, the following two were combined:

These tracks have since been updated to automatically fetch files from the MitoMap server. For all the details on how the data are processed and combined, see the MITOMAP makedoc.

Data Access

All source data can be found on the MITOMAP site.

The MITOMAP data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigBed files that can be downloaded from the respective file, e.g. MITOMAP Variants, on our download server. The data may also be explored interactively using our REST API.

The file for this track may also be locally explored using our tools bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g.,

bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/mitoMapVars.bb stdout

Credits

Thanks to Shiping Zhang and the entire MITOMAP resource for making these annotations available.

References

Lott MT, Leipzig JN, Derbeneva O, Xie HM, Chalkia D, Sarmady M, Procaccio V, Wallace DC. mtDNA Variation and Analysis Using Mitomap and Mitomaster. Curr Protoc Bioinformatics. 2013Dec;44(123):1.23.1-26. PMID: 25489354; PMC: PMC4257604