Public Data: TCGA Breast Cancer

We are pleased to announce that data from the following paper have been made available on GenomeSpace: 

The Cancer Genome Atlas Network.  Comprehensive molecular portraits of human breast tumors,  Nature, 2012;490:61-70. [doi:10.1038/nature11412]

The GenomeSpace mirror of this dataset includes all public level 3 and level 4 data from https://tcga-data.nci.nih.gov/docs/publications/brca_2012/

You can access the data in GenomeSpace at the path /Public/SharedData/Datasets/TCGA/Breast Cancer/.  (This requires a GenomeSpace login. If you don't have one, it's easy to register.)

Abstract:

We analyzed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, mRNA arrays, microRNA sequencing, and reverse phase protein arrays. Our ability to integrate information across platforms provided key insights into previously-defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at > 10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA, and MAP3K1 with the Luminal A subtype. We identified two novel protein expression-defined subgroups, possibly contributed by stromal/microenvironmental elements, and integrated analyses identified specific signaling pathways dominant in each molecular subtype including a HER2/p-HER2/HER1/p-HER1 signature within the HER2-Enriched expression subtype. Comparison of Basal-like breast tumors with high-grade Serous Ovarian tumors showed many molecular commonalities, suggesting a related etiology and similar therapeutic opportunities. The biologic finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biologic subtypes of breast cancer.