ArticlePLoS computational biology2017
High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 79 citations in OpenAlex.
- Article
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- Massively parallel sequencing of mitochondrial genome in primary open angle glaucoma identifies somatically acquired mitochondrial mutations in ocular tissue.Scientific reports · 2024Article
- CD4Scientific reports · 2024Article
- Our current understanding of the biological impact of endometrial cancer mtDNA genome mutations and their potential use as a biomarker.Frontiers in oncology · 2024Review
- MmisAT and MmisP: an efficient and accurate suite of variant analysis toolkit for primary mitochondrial diseases.Human genomics · 2023Article
- Wide diagnostic and genotypic spectrum in patients with suspected mitochondrial disease.Orphanet journal of rare diseases · 2023Article
- APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants.Nature communications · 2023Article
- Mitochondrial DNA Changes in Respiratory Complex I Genes in Brain Gliomas.Biomedicines · 2023Article
- Mitochondrial DNA variants in a cohort from Argentina with suspected Leber's hereditary optic neuropathy (LHON).PloS one · 2023Article
- Case report: A rare variant m.4135T>C in theFrontiers in genetics · 2023Article
- Mitochondrial DNA Changes in Genes of Respiratory Complexes III, IV and V Could Be Related to Brain Tumours in Humans.International journal of molecular sciences · 2022Article
- A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data.NAR genomics and bioinformatics · 2022Article
- Identification of Somatic Mitochondrial DNA Mutations, Heteroplasmy, and Increased Levels of Catenanes in Tumor Specimens Obtained from Three Endometrial Cancer Patients.Life (Basel, Switzerland) · 2022Article
- Mitochondrial DNA variation across 56,434 individuals in gnomAD.Genome research · 2022Article
- m.3685T > C is a novel mitochondrial DNA variant that causes Leigh syndrome.Cold Spring Harbor molecular case studies · 2022Article
- Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.Briefings in bioinformatics · 2022Article
- Genetic Alterations in Mitochondrial DNA Are Complementary to Nuclear DNA Mutations in Pheochromocytomas.Cancers · 2022Article
- Benchmarking the Effectiveness and Accuracy of Multiple Mitochondrial DNA Variant Callers: Practical Implications for Clinical Application.Frontiers in genetics · 2022Article
- Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks.Frontiers in bioinformatics · 2022Review
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
24,189 are all the possible non-synonymous amino acid changes potentially affecting the human mitochondrial DNA. Only a tiny subset was functionally evaluated with certainty so far, while the pathogenicity of the vast majority was only assessed in-silico by software predictors. Since these tools proved to be rather incongruent, we have designed and implemented APOGEE, a machine-learning algorithm that outperforms all existing prediction methods in estimating the harmfulness of mitochondrial non-synonymous genome variations. We provide a detailed description of the underlying algorithm, of the selected and manually curated training and test sets of variants, as well as of its classification ability.
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