Compiled by Cancer Dependency Map group, tool lets researchers identify cancer vulnerabilities.
Online portal aims to accelerate discoveries in precision cancer medicine
Researchers at the Broad Institute of MIT and Harvard have built a robust online portal that makes data and tools on the unique vulnerabilities of cancer cells easy for scientists across the globe to access and analyze. Built and compiled by the Broad’s Cancer Dependency Map, or DepMap, project team, the publicly available portal allows any researcher to explore and analyze data on genetic and pharmacologic dependencies and associated molecular features in cancer, which could pave the way for new precision therapies aimed at the specific vulnerabilities of cancer cells.
The new DepMap portal, available at https://depmap.org, brings together harmonized data from many publicly available resources and currently includes the following:
- Project Achilles, a Broad Cancer Program–based effort aimed at systematically identifying and cataloging genetic dependencies in cancer cell lines based on CRISPR-Cas9 and RNA interference (RNAi) loss-of-function screens.
- The Broad-Novartis Cancer Cell Line Encyclopedia, a compilation of gene expression, chromosomal copy number, and sequencing data from 947 human cancer cell lines.
- The Genomics of Drug Sensitivity in Cancer Project at the Wellcome Sanger Institute, conducted in collaboration with scientists at the Massachusetts General Hospital, which captures the sensitivities and responses of more than 1,000 genetically characterized human cancer cell lines to a wide range of anti-cancer therapeutics.
- The Novartis Institute for BioMedical Research’s Project DRIVE, a large-scale project involving RNAi screens in nearly 400 cancer cell lines for genetic dependencies with therapeutic potential.
The portal’s data, results, and visualization tools enable users — in particular, those with no computational background — to explore and find genetic targets for therapeutic development, and to develop a better understanding of the vulnerabilities of cancer.
The portal also incorporates a data exploration tool giving users an easy and convenient way to visualize available data (for example, to see the relationship between dependency and expression of a gene of interest). Importantly, the portal provides gene essentiality profiles for nearly every gene in the genome.
The DepMap portal also allows users to:
- Identify genetic drivers that have functional importance as potential drug targets;
- Understand dependency profiles at genome scale across more than 500 human cell lines, with more to be added; and
- Search for cell line models that best represent an investigator's research interests.
To accelerate cancer research further, the Broad Institute’s DepMap project team has committed to releasing cell line genomic information and genome-wide CRISPR-Cas9 loss-of-function screen data on a quarterly basis. They will also continue to add data and tools to the portal as they become available; tools for biomarker prediction and datasets on drug sensitivity from the Broad Institute Cancer Target Discovery and Development Center will be added soon.
Additional information about the DepMap project will be presented at the upcoming Association for Cancer Research (AACR) Annual Meeting by Dana-Farber Cancer Institute researcher and Broad institute member William Hahn in a talk titled, “Systematic Approaches to Identify Cancer Dependencies,” on April 15, 2018, at 1:05 PM CDT. AACR attendees are invited to learn more about the Broad Institute and the DepMap project at booth 3327.
For more about the Dependency Map Project and portal:
- Tsherniak A, Vazquez F, et al. Defining a cancer dependency map. Cell. Online July 27, 2017. DOI: 10.1016/j.cell.2017.06.010
- From the Broad Institute: Here there be dependencies: Putting cancers’ vulnerabilities on the map. Online July 27, 2017.
- From the Broad Institute: Editing false positives from cancer dependency maps drawn with CRISPR. Online October 30, 2017.