Study

METABRIC

Study ID Alternative Stable ID Type
EGAS00000000083 Genotype/Expression

Study Description

The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (CNVs, SNPs) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, although the landscape was dominated by cis and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP, and MAP2K4. Unsupervised analysis of paired DNA/RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, ER-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration 0152hotspots were found to modulate subgroup-specific gene networks, including a TCR ... (Show More)

Study Datasets 10 datasets.

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Dataset ID Description Technology Samples
EGAD00010000162
Illumina HT 12 IDATS
Illumina HT 12 2136
EGAD00010000164
Affymetrix 6.0 CEL files
Affymetrix SNP 6.0 1992
EGAD00010000210
Normalized expression data; discovery set
Illumina HT 12 997
EGAD00010000211
Normalized expression data; validation set
Illumina HT 12 995
EGAD00010000212
Normalized expression data; normals
Illumina HT 12 144
EGAD00010000213
Segmented (CBS) copy number aberrations (CNA); discovery set
Affymetrix SNP 6.0 997
EGAD00010000214
Segmented (CBS) copy number variants (CNV); discovery set
Affymetrix SNP 6.0 997
EGAD00010000215
Segmented (CBS) copy number aberrations (CNA); validation set
Affymetrix SNP 6.0 995
EGAD00010000216
Segmented (CBS) copy number variants (CNV); validation set
Affymetrix SNP 6.0 995
EGAD00010000217
Segmented (HMM) copy number aberrations (CNA); discovery set
Affymetrix SNP 6.0 997

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Publications

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