DepMap provides comprehensive genomic characterizations of human cancer cell lines, offering a wealth of data for understanding cancer biology. Datasets include detailed information on gene expression, copy number alterations, mutations and fusions, enabling researchers to explore the genetic vulnerabilities and potential therapeutic targets across genetically diverse cancer types.
With the Broad Institute’s Broad Clinical Labs, DepMap sequences cancer models and processes genomic data using published pipelines to generate high quality Omics data.
Sequencing
- 30X short-read WGS
- 50X WES
- 100X short-read RNA
Alignment/ Processing
- All data are aligned to hg38
- Initial check for file size and read count quality
- Germline structural variants are filtered out using gnomAD v4.1
- STR and SNP profiles confirmed
Standard Data Generation
Mutation pipeline
DepMap mutation calls are generated using Mutect2 and annotated and filtered downstream.
Detailed documentation can be found here: https://storage.googleapis.com/shared-portal-files/Tools/24Q4_Mutation_Pipeline_Documentation.pdf.
Copy Number pipelines
Relative Copy Number data from WGS/WES is generated by running the GATK copy number pipeline.
Tutorials and descriptions of this method can be found here:
- https://gatk.broadinstitute.org/hc/en-us/articles/360035531092–How-to-part-I-Sensitively-detect-copy-ratio-alterations-and-allelic-segments
- https://gatk.broadinstitute.org/hc/en-us/articles/360035531092--How-to-part-I-Sensitively-detect-copy-ratio-alterations-and-allelic-segments#1)
- https://gatk.broadinstitute.org/hc/en-us/articles/360035890011--How-to-part-II-Sensitively-detect-copy-ratio-alterations-and-allelic-segments
Absolute Copy Number data from WGS/WES is generated using PureCN: PureCN: copy number calling and SNV classification using targeted short read sequencing | Source Code for Biology and Medicine | Full Text.
Expression pipeline
DepMap expression data is quantified from RNAseq files using the GTEx pipelines.
A detailed description of the pipelines and tool versions can be found here: [GitHub - broadinstitute/depmap_omics:
- What you need to process the Quarterly DepMap-Omics releases from Terra: GitHub - broadinstitute/depmap_omics: What you need to process the Quarterly DepMap-Omics releases from Terra
Fusion pipeline
DepMap generates RNAseq based fusion calls using the STAR-Fusion pipeline. A comprehensive overview of how the STAR-Fusion pipeline works can be found here: Home · STAR-Fusion/STAR-Fusion Wiki · GitHub.
We run STAR-Fusion version 1.6.0 using the plug-n-play resources available in the STAR-Fusion docs for gencode v29. We run the fusion calling with default parameters except we add the --no_annotation_filter and --min_FFPM 0 arguments to prevent filtering.
