TCGA Breast Cancer Data Snapshot

This page provides links to the latest data freeze for the TCGA Breast Cancer Project.

Revisions Snapshot

  • Snapshot Version: 2.2
  • Snapshot Date: February 25, 2016

If you use this data please cite:

Ciriello, Gatza et al. (2015) Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell, 163, 2, 506-519

View the manuscript

Core Stats

View data within the cBio Portal

Select the Lobular Case Set to explore this dataset with the cBio Cancer Genomics Portal.

Data Status


Freeze Set, 3/26/14

Dataset #Samples CNA Exome-seq RNA-seq DNA-methylation miRNA RPPA ALL*
 ILC 127 127 127 127 127 (16 on 27K / 111 on 450K) 127 (26 on GA / 101 on HI-seq) 79 127
 IDC 490 490 490 490 490 (178 on 27K / 312 on 450K) 490 (158 on GA / 333 on HI-seq) 393 490
 Mixed 88 88 88 88 88 (36 on 27K / 52 on 450K) 88 (31 on GA / 57 on HI-seq) 72 88
 ILC Luminal-A 106 106 106 106 106 (12 on 27K / 94 on 450K) 106 (22 on GA / 84 on HI-seq) 65 106
 IDC Luminal-A 201 201 201 201 201 (70 on 27K / 131 on 450K) 201 (68 on GA / 134 on HI-seq) 158 201
* RPPA excluded

Additional Files


File Name Date Description
 BRCA817_sample_subgroups.xlsx 05/04/14 Excel file with case lists for classification based on histopathology (5 classes), mRNA expression (3), and DNA methylation (3).
 Gatza_TCGAlobular_5.13.2014.FINAL.pptx 05/13/14 Presentation at the TCGA symposium of the BRCA ILC project (Mike Gatza)
 ILC_figures_outline.pdf 07/22/14 Outline of manuscript figures (DRAFT)

Mutation Data


File Name Date Description
  RNA/DNA MAF (coding mutations only) 07/22/14 This file report all coding mutations across 993 sequenced breast tumors (the file non-coding mutations is available on the jamboree.

FOXA1 mutation analysis


(Giovanni Ciriello)

File Name Date Description
 FOXA1_mutation_diff_expression_analysis.xlsx 05/22/2014 Full list of FOXA1 mutations across 993 sequenced tumors and differential expression analysis between distinct FOXA1 types of mutations and wild type tumors.

RNA-seq


(Mike Gatza)

File Name Date Description
 ILC127_mRNAsubtype_calls_REVISED_06042014.xlsx 06/04/2014 RNA-seq based cluster assignment for ILC tumors.
 ILC_mRNAsubtypes_enriched_alterations.xlsx 06/04/2014 Subtype Enriched Alterations (SEA) analysis for RNA-seq based ILC subtypes.

Copy Number Alterations: GISTIC 2


(Hailei Zhang, Andy Cherniack)

Dataset #Samples File Size FireHose Run
 ILC 127 95 MB 4/5/2014
 IDC 490 219 MB 4/5/2014
 ILC Luminal-A 106 87 MB 4/5/2014
 IDC Luminal-A 201 125 MB 4/5/2014
 Mixed 88 91 MB 4/5/2014

Results also on FireHose


Consolidated GISTIC tables for IDC / ILC / IDC_lumA / ILC_lumA available here

Significantly Mutated Genes (MutSigCV)


(Hailei Zhang)

File Name Date Description
 BRCA_sig.genes.xlsx 25/2/2016 Significantly mutated genes (sig.genes) across 817 sequenced breast tumors. Sig.genes are reported for the whole dataset and all breast cancer subtypes presented in (Ciriello,Gatza et al. Cell 2015).

DNA Methylation


(Suhn Rhie, Peter Laird)

File Name Date Description
 179.Epigenetically.silenced.genes.TCGA.BRCA.050714.SR.txt 05/02/2014 List of epigenetically silenced genes.
 ILC.DNA.methylation.cluster.050714.SR.txt 05/02/2014 Cluster assignments for DNA methylation-based clustering of ILC tumors
 136.promoters.with.different.DNA.methylation.levels.ILC_LumA.vs.IDC_LumB.TCGA.050714.SR.txt 05/02/2014 List of genes whose promoter is differentially methylated between ILC LumA and IDC LumA

miRNA expression


(Reanne Bowlby)

File Name Date Description
 BRCA_DE_miRs.xlsx 05/02/2014 Comprehensive analysis of differentially expressed miRNA between all breast subgroups of interest.