We are working for an early release of a GDSC Matlab miner

PREVIEW - bioRxiv submission will follow this year (2020)

DrAGS | Mining cell line sensitivities to identify tumour genetic subtypes

Alessandro Esposito MRC Cancer Unit, University of Cambridge, Cambridge, United Kingdom e-mail: [email protected]

The collection of genomic and phenotypic data on cell lines are in constant growth, with consortia providing ever improving annotations and freely accessible web-based tools for data mining. While this wealth of information and analytical tools are already extremely useful to the broader community, researchers that are interested in specific queries not directly supported by data portals but lack specific bioinformatics expertise might not be able to gain advantage of these datasets. Here, we aim to describe and share a toolbox that permits researchers to define programmatically specific cohorts of cell lines on the bassi of easy to define but very articulated filters that operate on annotations of cell lines and mutations. We have therefore developed DrAGS (Drug sensitivity Association with Genetic Subtype), an open-source Matlab toolbox that permits researchers with basic skills in programming to generate complex queries to mine drug sensitivity responses. DrAGS consolidate annotations of cell lines and mutations across CRTP, GDSC, CCLE, COSMIC and Passport repositories and provide filters to define cohorts of cells harbouring mutations at specific genes, codons, with the capability to select mutations on the basis of zygosity, pathogenicity, frequency, and cell lines on the basis of tissue of origin, status and several other features. Comparisons between different cohorts are done by bootstrapping to evaluate custom statistics, zscore, pvals, vulcano plots, and FDR control.