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. 2019 Jan 8;47(D1):D1202-D1210.
doi: 10.1093/nar/gky1024.

HmtVar: a new resource for human mitochondrial variations and pathogenicity data

Roberto Preste  1 , Ornella Vitale  1 , Rosanna Clima  2 , Giuseppe Gasparre  2 , Marcella Attimonelli  1
Affiliations

HmtVar: a new resource for human mitochondrial variations and pathogenicity data

Roberto Preste et al. Nucleic Acids Res. .

Abstract

Interest in human mitochondrial genetic data is constantly increasing among both clinicians and researchers, due to the involvement of mitochondrial DNA (mtDNA) in a number of physiological and pathological processes. Thanks to new sequencing technologies and modern databases, the large amount of information on mtDNA variability may be exploited to gain insights into the relationship between mtDNA variants, phenotypes and diseases. To facilitate this process, we have developed the HmtVar resource, a variant-focused database that allows the exploration of a dataset of over 40 000 human mitochondrial variants. Mitochondrial variation data, initially gathered from the HmtDB platform, are integrated with in-house pathogenicity assessments based on various evaluation criteria and with a set of additional annotations from third-party resources. The result is a comprehensive collection of information of crucial importance for human mitochondrial variation studies and investigation of common and rare diseases in which the mitochondrion may be involved. HmtVar is accessible at https://www.hmtvar.uniba.it and data may be retrieved using either a web interface through the Query page or a state-of-the-art API for programmatic access.

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Figures

Figure 1.
Figure 1.
Total variants in HmtVar per locus type.
Figure 2.
Figure 2.
Percentage and number of potential and observed variants per locus type.
Figure 3.
Figure 3.
Percentage of variants with unassigned DS, with DS equal to 0 and with DS greater than 0, for each locus type.
Figure 4.
Figure 4.
CDS and tRNA variants annotated in HmtVar with available pathogenicity predictions.
Figure 5.
Figure 5.
HmtVar Variant Card: Main Info Tab. It reports the variant's basic information such as its location, the consequent amino acidic change for non-synonymous variants or specific structural details for tRNA variants, haplogroups and macro-haplogroups code if the variant is associated to a specific haplogroup according to Phylotree build 17 (http://phylotree.org/index.htm), as well as HmtVar pathogenicity prediction.
See this image and copyright information in PMC

References

    1. Gorman G.S., Chinnery P.F., DiMauro S., Hirano M., Koga Y., McFarland R., Suomalainen A., Thorburn D.R., Zeviani M., Turnbull D.M.. Mitochondrial diseases. Nat. Rev. Dis. Primers. 2016; 2:16080. - PubMed
    1. Hatakeyama H., Goto Y.-I.. Concise review: heteroplasmic mitochondrial DNA mutations and mitochondrial diseases: toward iPSC-Based disease modeling, drug discovery, and regenerative therapeutics. Stem Cells. 2016; 34:801–808. - PubMed
    1. Williams M., Caino M.C.. Mitochondrial dynamics in type 2 diabetes and cancer. Front. Endocrinol. (Lausanne). 2018; 9:211. - PMC - PubMed
    1. van Oven M., Kayser M.. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 2009; 30:E386–E394. - PubMed
    1. Lott M.T., Leipzig J.N., Derbeneva O., Xie H.M., Chalkia D., Sarmady M., Procaccio V., Wallace D.C.. mtDNA variation and analysis using mitomap and mitomaster. Curr. Protoc. Bioinformatics. 2013; 44:1–26. - PMC - PubMed

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