Category: Cancer drivers and genome interpretation

Genome Interpretation For Everybody
OpenCRAVAT Learn More Run on web Install yourself OpenCRAVAT is a dynamic software platform that annotates and prioritizes genomic alterations. Initially meant to share our lab's methodologies, it has evolved into a comprehensive resource offering approximately 300 tools, databases, and visualization options. Users can craft custom analysis pipelines via an adaptable filtering system. OpenCRAVAT is ...
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Variant interpretation in 3D

It has been hypothesized that hotspots may be cancer drug targets, biomarkers of cancer risk, and response to immunotherapy.  By mapping mutations onto 3D protein structures, it is possible to identify mutational “hotspots” that are not detectable on linear amino acid sequences. As part of the TCGA Ovarian Cancer working group, we identified 3D hotspots …

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Driver alterations in cancer genomes

In one of the first efforts to use machine learning to interpret tumor sequencing data, we developed CHASM, a supervised learning algorithm for predicting driver missense mutations. The algorithm integrated information about evolutionary conservation, amino acid biochemistry, protein context, structural predictions, and annotations, and we demonstrated that it improved on the current state-of-the-art in missense …

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