Hello, I am looking for a way to classify the cell lines in 3 categories (homozygously deleted/heterozygously deleted/WT, for my gene of interest) using the OmicsCNGene file and I found this conversation instructive. However, I am not sure to follow which threshold are you suggesting when using the OmicsCNGene file and not the segment profile file ? Did you update these threshold since this conversation happened and I missed it on the forum ? (and in this case I apologise) Thanks a lot in adva...

Broad scientists expand the DepMap by adding cancer organoids and demonstrate the models’ potential to fuel new discoveries.

For nearly a decade, the Cancer Dependency Map, or DepMap, at the Broad Institute has helped scientists uncover new cancer dependencies - the genetic changes some cancers need to thrive that can potentially be targeted by new cancer drugs. Now, project scientists have expanded the DepMap resource to include nearly 150 cancer models that grow as 3D cultures, also known as organoids or spheroids, across 10 cancer types. By integrating this data into the DepMap's existing dataset on more than a thousand 2D cancer models, the team has made the DepMap a more comprehensive resource for researchers that promises to reveal more drug targets and disease-driving mechanisms for more cancer types. In a study published in Nature, the team found new dependencies in the 3D models that weren't seen in the 2D ones, and generated dependency data on cancer subtypes that only grow in 3D, such as certain kinds of brain and gastrointestinal cancer. The findings provide valuable insights to researchers studying these "next-generation" 3D cancer models, and will help scientists choose between traditional and next-generation models for their work. The study appears alongside two related papers in the same journal by other groups, one led by the National Cancer...

For nearly a decade, the Cancer Dependency Map, or DepMap, at the Broad Institute has helped scientists uncover new cancer dependencies—the genetic changes some cancers need to thrive that can potentially be targeted by new cancer drugs.

Broad scientists expand the DepMap by adding cancer organoids and demonstrate the models’ potential to fuel new discoveries.

as shown by an analysis of DepMap data

Take advantage of more than 3,000 publicly available genomics data sets spanning millions of samples in the free academic R2 data science and discovery platform. R2 is designed for biomedical scientis...

Investigate the relationships between DepMap datasets