METABRIC data access committee

Dac ID Contact Person Email Access Information
EGAC00001000484 Marion Karniely metabric [at] cruk [dot] cam [dot] ac [dot] uk No additional information is available

This DAC controls 20 datasets:

Dataset ID Description Technology Samples
EGAD00001002115 Targeted sequencing of 173 genes in 2433 primary breast tumours. Data includes 2433 tumour samples, 523 adjacent normal (breast) samples and 127 blood samples. Libraries were prepared with Illumina's Nextera custom enrichment kit targetting all the exons of the most frequently mutated breast cancer genes. Libraries were multiplexed (48 libraries per lane) and sequenced on Illumina HiSeq 2000 (100bp paired-end reads). Somatic mutations were calling with a custom pipeline. We identified 40 mutation-driver (Mut-driver) genes, and determined associations between mutations, driver CNA profiles, clinical-pathological parameters and survival. We assessed the clonal states of Mut-driver mutations, and estimated levels of intra-tumour heterogeneity using mutant-allele fractions. The results emphasize the importance of genome-based stratification of breast cancer, and have important implications for designing therapeutic strategies. Referece: Pereira et al. (2016) The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nature Communications 3083
EGAD00001003342 Identification of fusion transcripts by RNA-sequencing and Whole genome sequencing of a breast cancer patient sample (METABRIC ID MB-0152) Illumina HiSeq 2000 3
EGAD00001007976 DNA methylation sequencing profiles of 1538 breast tumors and 244 normal breast tissues. Libraries were prepared using a custom Reduced Representation Bisulfite Sequencing pipeline. Sequencing was performed on the Illumina HiSeq 2500 (v4 chemistry), with single-end reads of 125 bp length. Multiplexing was conducted at the level of 8 samples per lane. FASTQ files are provided for 1538 breast tumors and 244 normal breast tissues. Reference: Batra et al. (2021). DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation. Illumina HiSeq 2500 1782
EGAD00010000158 Affymetrix 6.0 cel files Affymetrix SNP 6.0 473
EGAD00010000160 Illumina HT 12 IDATS 0
EGAD00010000162 Illumina HT 12 IDATS Illumina HT 12 0
EGAD00010000164 Affymetrix 6.0 CEL files Affymetrix SNP 6.0 0
EGAD00010000210 Normalized expression data; discovery set Illumina HT 12 1
EGAD00010000211 Normalized expression data; validation set Illumina HT 12 0
EGAD00010000212 Normalized expression data; normals Illumina HT 12 0
EGAD00010000213 Segmented (CBS) copy number aberrations (CNA); discovery set Affymetrix SNP 6.0 0
EGAD00010000214 Segmented (CBS) copy number variants (CNV); discovery set Affymetrix SNP 6.0 0
EGAD00010000215 Segmented (CBS) copy number aberrations (CNA); validation set Affymetrix SNP 6.0 0
EGAD00010000216 Segmented (CBS) copy number variants (CNV); validation set Affymetrix SNP 6.0 0
EGAD00010000217 Segmented (HMM) copy number aberrations (CNA); discovery set Affymetrix SNP 6.0 0
EGAD00010000266 Metabric breast cancer samples (Genotype raw data) Affymetrix SNP 6.0 543
EGAD00010000268 Metabric breast cancer samples (Expression raw data) Illumina HT 12 543
EGAD00010000270 Metabric breast cancer samples (Images) Aperio image - H&E stained tissue_section 564
EGAD00010000436 Illumina HT 12 IDAT files Illumina HT 12 1302
EGAD00010000442 Affymetrix SNP 6.0 CEL files Affymetrix_SNP6_raw 1302