mvTool v.6: The mtDNA variant reference based on 316,530 whole genome sequences
February 22, 2021 Dr. Lishuang SHEN 0
The mvTool is upgraded to version 6.
The major upgrade in version 6 is the addition of gnoMAD mtDNA variant data from 56,434 whole genome samples.
MSeqDR constructs the mtDNA meta-population allele frequency reference, which provides position-specific variant information for up to 346,000 individuals at some positions. The maximum WGS coverage is 260,096, the maximum WGS+WES coverage is about 346,000. Data were derived from mito-WGS or from WES.
The mvTool mtDNA annotation report is updated in content and layout to reflect the addition of the gnoMAD and HelixMTdb data. For single variant annotation, a new report button supports converting the annotation into vertical tables for alternative views in different directions.
The major mitochondrial DNA variant data sources:
1. Mitomap: hand-curated maintained over 20 years by the expert team of Prof. Doug Wallace and Marie Lott.
Description by the authors:
“2021 Update #1: Ok Jan 15, 2021 we added 164 new full-length (FL) and 206 new control region (CR) GenBank sequences to our database. This brings our total number of FL sequences to 51,836 and the number of CR sequences to 74,866. Our SNVs now total 19,403.”
2. gnoMAD mtDNA variant data from 56,434 whole genome samples.
This high-quality, expert-curated dataset will be a must-go reference population dataset for the community.
The description by the gnoMAD team:
“Mitochondrial DNA (mtDNA) variants for gnomAD are now available for the first time! We have called mtDNA variants for 56,434 whole genome samples in the v3.1 release. This initial release includes population frequencies for 10,850 unique mtDNA variants defined at more than half of all mtDNA bases. The vast majority of variant calls (98%) are homoplasmic or near homoplasmic, whereas 2% are heteroplasmic.”
3. HelixMTdb for 196,554 unrelated healthy individuals, which includes 15,035 unique variants. The HelixMTdb database reflects aggregated and de-identified mitochondrial DNA variants observed in individuals sequenced at Helix:
Selective constraints and pathogenicity of mitochondrial DNA variants inferred from a novel database of 196,554 unrelated individuals
Alexandre Bolze, Fernando Mendez, Simon White, Francisco Tanudjaja, Magnus Isaksson, Misha Rashkin, Johnathan Bowes, Elizabeth T. Cirulli, William J. Metcalf, Joseph J. Grzymski, William Lee, James T. Lu, Nicole L. Washington
4. HmtVar – a manually-curated database offering variability and pathogenicity information about mtDNA variants.
HmtVar: a new resource for human mitochondrial variations and pathogenicity data
Roberto Preste, Ornella Vitale, Rosanna Clima, Giuseppe Gasparre, and Marcella Attimonelli
PMC6323908, PMID_ 30371888
Kaviar: an accessible system for testing SNV novelty.
Glusman G1, Caballero J, Mauldin DE, Hood L, Roach JC
Bioinformatics (Oxford, England), 27 Sep 2011, 27(22):3216-3217
DOI: 10.1093/bioinformatics/btr540 PMID: 21965822 PMCID: PMC3208392
Categories: MSeqDr.org News, updates, media report
- gnoMAD shares mtDNA variant data from 56,434 whole genome samples
- mvTool v.6: The mtDNA variant reference based on 316,530 whole genome sequences
- MSeqDR is migrated to a new webserver at CHLA
- International Research Team Develops Consensus Variant Classification Guidelines for Genomic Variants in Mitochondrial DNA
- mvTool v.5: New report layout and new mtDNA variant data from 200,000 healthy people
- Recent publications from MSeqDR supported by the UMDF and NIH grants
- ClinGen / ClinVar – MSeqDR Working Groups & Expert Panels
- ClinGen approved the MSeqDR Consortium mitochondrial DNA Sequence Variant Interpretation (SVI) specifications
- U24 Mitochondrial Diseases Expert Panel is establishing 63 genes’ Leigh Disease associations at ClinGen
- MSeqDr joins FAIRsharing – A curated resource on data and metadata standards