ArticleNature communications2023
APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 34 citations in OpenAlex.
- Advances in diagnosis of mitochondrial dysfunction and primary mitochondrial disease.Disease models & mechanisms · 2026Review
- The mitogenome diversity of Alpine Rendena cattle: new clues on its maternal origin and the complex substructure of haplogroup T3.Genetics, selection, evolution : GSE · 2026Article
- Mitochondrial genetic variation across tissues of the human body.Nucleic acids research · 2026Article
- Article
- Comprehensive evaluation of ACMG/AMP-based variant classification tools.Bioinformatics (Oxford, England) · 2026Article
- The Loss of Complex I in Renal Oncocytoma Is Associated with Defective Mitophagy Due to Lysosomal Dysfunction.International journal of molecular sciences · 2025Article
- Mitochondrial DNA variant detection in over 6,500 rare disease families by the systematic analysis of exome and genome sequencing data resolves undiagnosed cases.HGG advances · 2025Article
- Mitochondrial haplogroup A2 is associated with increased COVID-19 mortality in an admixed Brazilian population.Scientific reports · 2025Article
- Investigating the dual role of mitochondrial and nuclear genome variants in pediatric cardiomyopathies.Scientific reports · 2025Article
- Mitochondrial DNA variants revealed by whole exome sequencing: from screening to diagnosis and follow-up.Neurogenetics · 2025Article
- The landscape of rare mitochondrial DNA variants in sudden cardiac death: A potential role for ATP synthase.Heliyon · 2025Article
- Pathogenic mitochondrial DNA variants are associated with response to anti-VEGF therapy in ovarian cancer PDX models.Journal of experimental & clinical cancer research : CR · 2024Article
- Variant load of mitochondrial DNA in single human mesenchymal stem cells.Scientific reports · 2024Article
- mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics.Nucleic acids research · 2024Article
- A novel mitochondrial DNA variant inMolecular genetics and metabolism reports · 2024Article
- Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue.Biomolecules · 2024Article
- A machine learning-based predictive model of causality in orthopaedic medical malpractice cases in China.PloS one · 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
- Mutational profiling of mitochondrial DNA reveals an epithelial ovarian cancer-specific evolutionary pattern contributing to high oxidative metabolism.Clinical and translational medicine · 2024Article
- APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants.Nature communications · 2023Article
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Authors and funding
15 authors at 4 institutions in 3 countries.
Funding
Abstract
Mitochondrial dysfunction has pleiotropic effects and is frequently caused by mitochondrial DNA mutations. However, factors such as significant variability in clinical manifestations make interpreting the pathogenicity of variants in the mitochondrial genome challenging. Here, we present APOGEE 2, a mitochondrially-centered ensemble method designed to improve the accuracy of pathogenicity predictions for interpreting missense mitochondrial variants. Built on the joint consensus recommendations by the American College of Medical Genetics and Genomics/Association for Molecular Pathology, APOGEE 2 features an improved machine learning method and a curated training set for enhanced performance metrics. It offers region-wise assessments of genome fragility and mechanistic analyses of specific amino acids that cause perceptible long-range effects on protein structure. With clinical and research use in mind, APOGEE 2 scores and pathogenicity probabilities are precompiled and available in MitImpact. APOGEE 2's ability to address challenges in interpreting mitochondrial missense variants makes it an essential tool in the field of mitochondrial genetics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.