CellMiner cross-database (CellMinerCDB) version 2.2 for explorations of patient-derived cancer cell line pharmacogenomics

Abstract CellMiner Cross-Database (CellMinerCDB) (https://discover.nci.nih.gov/cellminercdb/) is an established interactive application providing direct access and enabling exploration of cancer cell line pharmacogenomics without extensive programming experience. Data are compiled from many sources, including the National Cancer Institute(NCI), Broad Institute Dependency Map (DepMap), Sanger/MGH Genomics of DrugSensitivity in Cancer (GDSC), MD Anderson Cell Lines Project (MCLP), andNational Center for Advancing Translational Sciences (NCATS). In the version 2.2 update, our collection has expanded to pharmacogenomics data for 1916 cancer cell lines and over 25 000 drugs. Drug screening data include many additional compounds for potential drug repurposing from the Broad PRISM, NCATS, and NCI. The user interface facilitates uncovering specific samples of interest and identifying drug and cell lines across databases. We also expanded the annotations for cross-referencing other databases and downloading our data for further cancer biology and drug discovery studies. Herein, we provide use cases for CellMinerCDB, including (i) data reproducibility given overlaps of cell lines, genes, and drugs across databases; (ii) candidate biomarker discovery; and (iii) cross-dataset analyses.