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Protocols

HmtDB specifications

Information


Unique identifier OMICS_04548
Name HmtDB
Alternative name Human Mitochondrial Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Marcella Attimonelli

Publications for Human Mitochondrial Database

HmtDB citations

 (15)
library_books

Peculiar combinations of individually non pathogenic missense mitochondrial DNA variants cause low penetrance Leber’s hereditary optic neuropathy

2018
PLoS Genet
PMCID: 5828459
PMID: 29444077
DOI: 10.1371/journal.pgen.1007210

[…] eviously reported []. Population frequencies of missense mutations and the mtDNA backgrounds on which they were observed were recovered from two public databases, Mitomap (http://www.mitomap.org) and HmtDB (http://www.hmtdb.uniba.it) [,]. Haplogroup affiliations of mitogenomes were assigned according to PhyloTree (www.phylotree.org) []. […]

call_split

Examining the role of common and rare mitochondrial variants in schizophrenia

2018
PLoS One
PMCID: 5784966
PMID: 29370225
DOI: 10.1371/journal.pone.0191153
call_split See protocol

[…] o gain data for another 30 common SNPs giving us 71 in total (considering post-imputation filters of “info” score > 0.3 and MAF > 1%). We downloaded 7,141 public European mitochondrial sequences from Human Mitochondrial DataBase [] and used them as reference panel (SNP N = 188 after filtered by MAF > 1%). Imputation was performed using IMPUTE2 v.2 software [], following the instructions for chromo […]

library_books

Pathological and molecular diagnosis of bilateral inguinal lymph nodes metastases from low grade endometrial adenocarcinoma: a case report with review of the literature

2018
BMC Cancer
PMCID: 5751855
PMID: 29295713
DOI: 10.1186/s12885-017-3944-7

[…] The informative nature of mitochondrial mutations was ascertained by sequencing mitochondrial DNA from saliva.Sequence analysis was performed with MToolBox [] and the genomes were deposited in public human mitochondrial database HmtDB [] with the following identifiers: endometrial tumor: PA_EU_IT_0271, metastasis: PA_EU_IT_0272, saliva: PA_EU_IT_0273. The analysis revealed the presence of several […]

library_books

Renal oncocytoma characterized by the defective complex I of the respiratory chain boosts the synthesis of the ROS scavenger glutathione

2017
Oncotarget
PMCID: 5739687
PMID: 29285300
DOI: 10.18632/oncotarget.22413

[…] oplasmic mutation, neither contributed in defining other haplogroups nor was annotated in MitoMAP [], implying that it was novel, and had very low nucleotide variability (0.00031) as estimated in the HmtDB database [] and in the tracks of MSeqDR Mitochondrial Disease pathogenic mutation variant [].In the case of 8 variants with non-protein-coding events, 7 mapped in the MT-DLOOP region (, GM_nonco […]

library_books

Packaging and transfer of mitochondrial DNA via exosomes regulate escape from dormancy in hormonal therapy resistant breast cancer

2017
Proc Natl Acad Sci U S A
PMCID: 5664494
PMID: 29073103
DOI: 10.1073/pnas.1704862114

[…] described (). Electropherograms were analyzed by SeqScape software (Applied Biosystems). Functional annotation was performed by applying previously described methods () and consulting MitoMap () and HmtDB (). Mu-mtDNA was also sequenced using a specific 46-amplicon PCR technique (this method is under patent approval, and its details cannot be included). Long-range PCR and qPCR () were used to amp […]

library_books

Identification and analysis of mtDNA genomes attributed to Finns reveal long stagnant demographic trends obscured in the total diversity

2017
Sci Rep
PMCID: 5522469
PMID: 28733587
DOI: 10.1038/s41598-017-05673-7

[…] Complete modern mtDNA genomes from Finland were obtained through GenBank searches, HmtDB searches, and from published literature, including information on the population of origin. Altogether 843 complete Finnish sequences were retrieved (Table  and Supplementary Dataset File). Seq […]

Citations

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HmtDB institution(s)
Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy; Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, Bologna, Italy; European Bioinformatics Institute EMBL Outstation - Hinxton, Wellcome Trust Genome Campus, Cambridge, UK; IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab Bari, Italy; Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Kalmar, Sweden; Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
HmtDB funding source(s)
FP7 ITN-People Marie Curie Action grant (MEET - Mitochondrial European Educational Training, GA #317433), The Italian Association for Cancer Research (AIRC) (#IG14242), Italian Ministry of Health (GR-2013-02356666), Worldwide Cancer Research UK grant DHOMOS.

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