Cancer Program Data Resources

Melanoma Genome Sequencing

Whole genome sequencing of 25 metastatic melanoma tumors with matched-normals.

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.

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).

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.

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.

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.

TCGA Tumorscape

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.

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, 2011).
The purpose of the Matrisome Project web page is to provide information and resources relevant to research on ECM proteins and to be a platform for deploying data collections, methods, and protocols. Our aim is to facilitate the use of our protocols by other scientists and to allow their widespread use in future studies.

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.



Genes, Cancers, and DNA Mutations