ArticleBioinformatics (Oxford, England)2021
Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Interpreting human genetic variation at atomic resolution.Nature genetics · 2026Review
- Mutational landscapes of HNF MODY gene products display a wide distribution with functional implications.Endocrine connections · 2025Review
- Mutant KRAS inhibitors enter the scene of precision therapeutics for pancreatic cancer.Journal of gastrointestinal oncology · 2024Article
- Beyond Structural Bioinformatics for Genomics with Dynamics Characterization of an Expanded KRAS Mutational Landscape.bioRxiv : the preprint server for biology · 2023Article
- Beyond structural bioinformatics for genomics with dynamics characterization of an expanded KRAS mutational landscape.Computational and structural biotechnology journal · 2023Article
- A multi-layered computational structural genomics approach enhances domain-specific interpretation of Kleefstra syndrome variants in EHMT1.Computational and structural biotechnology journal · 2023Article
- Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome.Genome medicine · 2022Article
- Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics.Computational and structural biotechnology journal · 2022Article
- PJAMIA open · 2021Article
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Authors and funding
4 authors.
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Abstract
motivationProtein-coding genetic alterations are frequently observed in Clinical Genetics, but the high yield of variants of uncertain significance remains a limitation in decision making. RAS-family GTPases are cancer drivers, but only 54 variants, across all family members, fall within well-known hotspots. However, extensive sequencing has identified 881 non-hotspot variants for which significance remains to be investigated.
resultsHere, we evaluate 935 missense variants from seven RAS genes, observed in cancer, RASopathies and the healthy adult population. We characterized hotspot variants, previously studied experimentally, using 63 sequence- and 3D structure-based scores, chosen by their breadth of biophysical properties. Applying scores that display best correlation with experimental measures, we report new valuable mechanistic inferences for both hot-spot and non-hotspot variants. Moreover, we demonstrate that 3D scores have little-to-no correlation with those based on DNA sequence, which are commonly used in Clinical Genetics. Thus, combined, these new knowledge bear significant relevance. AVAILABILITY AND IMPLEMENTATION: All genomic and 3D scores, and markdown for generating figures, are provided in our supplemental data. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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