ArticleGenetics in medicine : official journal of the American College of Medical Genetics2022
The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK).
Article in Genetics in medicine : official journal of the American College of Medical Genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 17 citations in OpenAlex.
- Natural history of retinitis pigmentosa based on genotype, vitamin A/E supplementation, and an electroretinogram biomarker.JCI insight · 2023Trial
- Structure-Based Network Analysis of AlphaFold Structure Predictions Identifies Putative Causative Variants of Inherited Retinal Disease.Investigative ophthalmology & visual science · 2026Article
- Genetic Testing in Inherited Retinal Disease: Current Strategies and Future Directions.Journal of personalized medicine · 2026Review
- Variants in the ciliopathy gene SCLT1 are associated with non-syndromic and syndromic retinal degeneration of variable severity.NPJ genomic medicine · 2026Article
- The landscape of variants in pre-mRNA-processing factor genes in an Irish cohort.Genetics in medicine open · 2026Article
- Elucidating photoreceptor gene function with in-vivo CRISPR knock-out perturbation assay.Research square · 2025Article
- Biallelic null variants in C19orf44 cause a unique late-onset retinal dystrophy phenotype characterized by patchy perifoveal chorioretinal atrophy.Genetics in medicine : official journal of the American College of Medical Genetics · 2025Article
- Deciphering the Genetic Basis of Degenerative and Developmental Eye Disorders in 50 Pakistani Consanguineous Families Using Whole-Exome Sequencing.International journal of molecular sciences · 2025Article
- Novel Potentially Pathogenic Variants in TBC1D32 Cause Non-syndromic Rod-Cone Degeneration.Advances in experimental medicine and biology · 2025Article
- Coding and non-coding variants in the ciliopathy gene CFAP410 cause early-onset non-syndromic retinal degeneration.NPJ genomic medicine · 2024Article
- Structure-based network analysis predicts pathogenic variants in human proteins associated with inherited retinal disease.NPJ genomic medicine · 2024Article
- Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease.American journal of human genetics · 2024Article
- Clinician-Driven Reanalysis of Exome Sequencing Data From Patients With Inherited Retinal Diseases.JAMA network open · 2024Article
- Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease.medRxiv : the preprint server for health sciences · 2023Article
- Challenges and Opportunities in the Genetic Analysis of Inherited Retinal Dystrophies in Africa, a Literature Review.Journal of personalized medicine · 2023Review
- Identification of a novel large multigene deletion and a frameshift indel inCold Spring Harbor molecular case studies · 2022Article
- StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants.American journal of human genetics · 2022Article
Corrections and comments
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Authors and funding
17 authors at 8 institutions in 1 country.
Funding
Abstract
purposeIn Mendelian disease diagnosis, variant analysis is a repetitive, error-prone, and time consuming process. To address this, we have developed the Mendelian Analysis Toolkit (MATK), a configurable, automated variant ranking program.
methodsMATK aggregates variant information from multiple annotation sources and uses expert-designed rules with parameterized weights to produce a ranked list of potentially causal solutions. MATK performance was measured by a comparison between MATK-aided and human-domain expert analyses of 1060 families with inherited retinal degeneration (IRD), analyzed using an IRD-specific gene panel (589 individuals) and exome sequencing (471 families).
resultsWhen comparing MATK-assisted analysis with expert curation in both the IRD-specific gene panel and exome sequencing (1060 subjects), 97.3% of potential solutions found by experts were also identified by the MATK-assisted analysis (541 solutions identified with MATK of 556 solutions found by conventional analysis). Furthermore, MATK-assisted analysis identified 114 additional potential solutions from the 504 cases unsolved by conventional analysis.
conclusionMATK expedites the process of identification of likely solving variants in Mendelian traits, and reduces variability stemming from human error and researcher bias. MATK facilitates data reanalysis to keep up with the constantly improving annotation sources and next-generation sequencing processing pipelines. The software is open source and available at https://gitlab.com/matthew_maher/mendelanalysis.
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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.