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Latest Release DepMap Public 18Q4 | November 2018
The DepMap Public 18Q4 release includes CRISPR screen and omics datasets expanded to include new cell lines. The Avana CRISPR screen dataset is expanded to include 517 cell lines. Mutation, indel, copy number and gene expression data are also expanded to include new lines in Avana dataset. As our screening efforts continue, we will be releasing additional cancer dependency data on a quarterly basis.
The CRISPR screen uses the Avana CRISPR-Cas9 genome-scale knockout library, and descriptions of the experimental methods and the CERES algorithm are published in here. The previously published line ACH-000005 has been dropped for slipping over the edge of QC failure.
Copy number and mutation data for some cell lines were based on Sanger Institute whole exome sequencing data (COSMIC: http://cancer.sanger.ac.uk/cell_lines, EGA accession number: EGAD00001001039) reprocessed using CCLE pipelines.
For 18Q4, we have added the Variant_annotation column to depmap_18Q4_mutation_calls.csv. This groups mutations according to the Variant_Classication column, and corresponds to the coloring of mutations in the portal. See here for details.
Copy NumberPublic 18Q4
Cell Line Metadata
CRISPR(Avana) Public 18Q4
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Combined RNAi(Broad, Novartis, Marcotte)
Please cite the following publications when using these datasetsFor CRISPR datasets:
Broad Institute Cancer Dependency Map; Cancer Data Science (2018): Cancer Dependency Map, CRISPR Avana dataset 18Q4 (Avana_public_18Q4). figshare. Fileset. doi:10.6084/m9.figshare.7270880.v1
Robin M. Meyers, Jordan G. Bryan, James M. McFarland, Barbara A. Weir, ... David E. Root, William C. Hahn, Aviad Tsherniak. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics 2017 October 49:1779–1784. doi:10.1038/ng.3984For omics datasets:
Cancer Cell Line Encyclopedia Consortium, and Genomics of Drug Sensitivity in Cancer Consortium. 2015. Pharmacogenomic Agreement between Two Cancer Cell Line Data Sets. Nature 528 (7580):84–87. https://doi.org/10.1038/nature15736.
Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, William R. Sellers, Robert Schlegel, Levi A. Garraway, et. al. 2012. The Cancer Cell Line Encyclopedia Enables Predictive Modelling of Anticancer Drug Sensitivity. Nature 483 (7391):603–7. https://doi.org/10.1038/nature11003.For the RNAi dataset:
James M. McFarland, Zandra V. Ho, Guillaume Kugener, Joshua M. Dempster, Phillip G. Montgomery, Jordan G. Bryan, John M. Krill-Burger, Thomas M. Green, Francisca Vazquez, Jesse S. Boehm, Todd R. Golub, William C. Hahn, David E. Root, Aviad Tsherniak. (2018). Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nature Communications 9, 1. https://doi.org/10.1038/s41467-018-06916-5