Cancer Program Data Resources
Tumorscape is designed to facilitate the use and understanding of high resolution copy number data amassed from multiple cancer types. It enables download and interactive viewing of 3131 cancer copy-number profiles across several dozen cancer types; gene-level queries to determine the rate and significance of alteration of every gene; and cancer-type-level queries to identify the significant regions of copy-number alteration.
Genes, Cancers, and DNA Mutations
|Tumor microenvironment and Drug resistance||
A high-throughput co-culture system was developed to systematically assay the ability of stromal cells to influence the innate resistance of 45 cancer cell lines to anti-cancer drugs. Protein antibody microarrays were used to assess the presence of hundreds of secreted proteins in the preconditioned media of the stromal cells. This database led to the identification of HGF as a cytokine that can induce resistance of Melanoma tumors with BRAF mutations to RAF inhibition therapy.
|The Matrisome Project||
The Matrisome Project is a collaborative effort between scientists from the Hynes Lab at the Koch Institute for Integrative Cancer Research at MIT and the Broad Institute of MIT and Harvard, aimed at defining bioinformatically and experimentally the ensemble of genes encoding the "matrisome", i.e. the ensemble of extracellular matrix and ECM-associated proteins (Naba et al, 2012).
TCGA Tumorscape is designed to facilitate the use and understanding of high resolution copy number data amassed from multiple cancer types (all generated through TCGA). It enables download and interactive viewing of cancer copy-number profiles across several dozen cancer types; gene-level queries to determine the rate and significance of alteration of every gene; and cancer-type-level queries to identify the significant regions of copy-number alteration.
|TCGA Data and Analyses (Broad GDAC)||
The Broad GDAC Firehose provides TCGA Level 3 data and Level 4 analyses packaged in a form amenable to immediate algorithmic analysis. This enables a wide range of cancer biologists, clinical investigators, and genome and computational scientists to easily incorporate TCGA into the backdrop of ongoing research. Please see FireBrowse for interactive exploration and programmatic access to the TCGA data and analyses performed by the Broad GDAC.
|Prostate Cancer Genome Sequencing||
Exome sequencing and copy number profiling were performed on 112 primary prostate tumor / normal DNA pairs. Novel significantly mutated genes were identified, including SPOP, MED12 and FOXA1.
|NF1 and RAF inhibitor resistance||
Using whole-genome shRNA screening, this work identifies functional loss of NF1 as a mediator of resistance to RAF inhibitors in B-RAFV600E-mutant cancers. Furthermore, we nominate new therapeutic modalities to treat this mechanism of resistance.
|Multiple Myeloma Genomics Portal||
The Multiple Myeloma Genomics Portal is a part of the Multiple Myeloma Genomics Initiative, a collaboration of The Multiple Myeloma Research Consortium, The Broad Institute of MIT and Harvard, and the Translational Genomics Research Institute (TGen).
|Melanoma Genomics Portal||
Here, we describe a comprehensive genomic analysis of 101 melanoma short-term cultures and cell lines. Using an analytic approach designed to enrich for putative “driver” events, we show that cultured melanoma cells encompass the spectrum of significant genomic alterations present in primary tumors.