Explore the Cancer Dependency Map

Chronos CRISPR Data This quarter, we're introducing a successor to CERES named Chronos. Chronos is based on a cell population dynamics model and provides several improvements over CERES. You can read more about the model and how we evaluated it in our preprint, as well as on this blog post. This quarter, Chronos will be available as an option for downloading or exploring in the portal. Next quarter, we plan to make it the default CRISPR dataset in the DepMap portal for gene cards and other tools.

Revised Dataset Names This quarter we've standardized the nomenclature used for identifying dependency datasets in Data Explorer and other portions of the portal. Please be aware that these names have changed. For example, the dataset which was previously labeled "CRISPR (Avana) Public 21Q1" is now named "CRISPR (DepMap 21Q1 Public, CERES)".

Integrated CRISPR Datasets We received a lot of questions about whether we will ever have the Broad and Sanger CRISPR screens together in one dataset. We're happy to say the answer is yes! Beginning this quarter, all new versions of the Achilles datasets will be available with Sanger's Project Score dataset integrated. We've produced a preprint describing our methodology.

We've corrected a mistake where "DepMap Public 20Q4 v2" on the downloads page was incorrectly downloading files from the "DepMap Public 20Q4" release. The download links have been corrected.

We identified issues with several files in the “DepMap Public 20Q4” dataset and have loaded a new release labeled "DepMap Public 20Q4 v2", which addresses those issues, into the portal. See this post on the forum for more details..

New data in 20Q4 We are happy to report that we have released CRISPR data for 19 lines this quarter to bring our total number of cell lines with Avana CRISPR data to 808.

Target validation protocols Our most commonly used target validation protocols are now public at protocols.io - an open repository of protocols.

Whole Genome Sequencing (WGS) in DepMap We have begun generating WGS rather than WES for cell lines. Although only CN and exonic mutations are reported for this release, we are working to add additional data from WGS in future releases.

Removing Cell Lines from all Omics datasets We are removing ACH-001189, ACH-002303, ACH-002315, ACH-002341 from the all omics datasets since they are duplicate entries.

Y Chromosome Missing - CN dataset Y chromosome was missing from copy number calls in some cell lines. This issue has been resolved in the new release by using a new panel of normal samples. For some cell lines, minor changes have occurred to overall copy number calls in all chromosomes. Lines which significantly deviated in their autosomal CNV from previous release have not been incorporated and are being assessed further for future release.

Removal of cell lines - expression and fusion datasets We are removing 10 lines that did not pass QC in the expression and fusion datasets. Please see details in the README files in the Downloads page.