Elaine R Mardis | bioRxiv Science

bioRxiv2016

CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer.

CIViC is an expert crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer (www.civicdb.org) describing the therapeutic, prognostic, and diagnostic relevance of inherited and somatic variants of all types. CIViC is committed to open source code, open access content, public application programming interfaces (APIs), and provenance of supporting evidence to allow for the transparent creation of current and accurate variant interpretations for use in cancer precision medicine.

Cancer Biology↗

bioRxiv2016

Visualizing tumor evolution with the fishplot package for R

BackgroundMassively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. Easily interpretable data visualizations can greatly aid these studies, especially in cases with multiple timepoints. Current data visualization methods are typically manual and laborious, and often only approximate subclonal fractions.\n\nResultsWe have developed an R package that accurately and intuitively displays changes in clonal structure over time. It requires simple input data and produces illustrative and easy-to-interpret graphs suitable for diagnosis, presentation, and publication.\n\nConclusionsThe simplicity, power, and flexibility of this tool make it valuable for visualizing tumor evolution, and it has potential utility in both research and clinical settings. Fishplot is available at https://github.com/chrisamiller/fishplot

Bioinformatics↗