Announcing the 25Q3 Release

Announcements
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25Q3 DepMap Release Notes

We’re excited to announce the release of new DepMap data and a new tool, Context Explorer, to help you perform context-specific analyses. We’ve also made important updates to our Omics and CRISPR pipelines. Please read the release note below for more information.

NEW DEPMAP DATASETS AND FEATURES

Standard Release Data

  • We’ve added 9 new paired WGS/RNA profiles and 3 new genome-wide CRISPR KO screens in rare and pediatric cancers, and 7 new Sanger KY screens.

BioGRID Open Repository of CRISPR Screens (https://orcs.thebiogrid.org/)

  • A new BioGrid dataset is available on the portal containing the results of 22 genome-scale CRISPR knockout screens using TKOv3 Cas9 or Brunello Cas9 libraries.

  • This dataset is currently available for download only.

NEW TOOLS

  • Context Explorer

    • Context Explorer enables researchers to explore enriched genetic dependencies and compound sensitivities across cancer lineages and subtypes. Available contexts include the full depth of Oncotree, as well as a new parallel “Molecular Subtypes” disease hierarchy. These correspond to the subtypes available in the new SubtypeTree.csv file.

    • Access Context Explorer by navigating to the Tools dropdown menu.

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CRISPR PIPELINE UPDATES

  • Sequencing technology batching for Chronos Runs

    • Previously, we discovered a batch effect between sequencing technologies in Humagne-CD library screens. In order to resolve this batch effect, we have updated our batching strategy for Chronos to include sequencing technology information. In this release, NovaSeq and HiSeq screens in the Humagne-CD library were considered separate screen_type batches and underwent chronos library correction.

    • Previously, Chronos batches followed library-screen_type:

      • Avana-2D

      • Humagne-CD-2D

      • KY-2D

    • Updated Chronos batches are defined with an updated screen_type definition that includes sequencing technology:

      • Avana-2D

      • Humagne-CD-2D-HiSeq

      • Humagne-CD-2D-NovaSeq

      • KY-2D

    • To prevent undercorrection of the library effect of Humagne-CD screens, Chronos has also been updated to regularize towards the mean gene effect that is weighted by the number of screens in each batch. The updated sequencing technology batching strategy does not affect the format of released files.

OMICS PIPELINE UPDATES

  • Users will notice the following streamlined Omics outputs for ease of use and to avoid redundancy:

    • All output tables will now have the following metadata columns:

      • ModelID (ACH-): Represents a cell line model

      • IsDefaultEntryForModel [Yes/No]: A “Yes” in this field indicates the default selection for the Model. All model-level outputs represented visually in the portal will correspond to IsDefaultEntryForModel == “Yes”

      • ModelConditionID (MC-): Represents a model in a specific experimental condition.

      • IsDefaultForMC [Yes/No]: A “Yes” in this field indicates the default selection for the Model Condition.

      • SequencingID (CDS-): This ID uniquely identifies a sequencing output. This field can be used to uniquely identify specific NGS data outputs when needed.

    • As of 25Q3 release, profile-level outputs will no longer be hosted.

  • Mutation Pipeline

    • Removed Columns: LofGeneName, LofGeneId, LofNumberOfTranscriptsInGene, LofPercentOfTranscriptsAffected, DidaID, and DidaName will no longer be included in mutation files

  • New column in OmicsProfile.csv:

    • SequencingDate - indicates the date of a genomic sequence.

PORTAL UPDATES

  • Bug fixes and minor updates

    • Celligner has been updated to display data indexed by Model Condition ID instead of Profile ID. This is consistent with the indexing changes being made to Omics file downloads.

    • Performance improvements to support larger datasets in interactive tools