METABRIC data access committee

Contact Information

Marion Karniely
metabric@cruk.cam.ac.uk

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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		-
EGAD00010000162	Illumina HT 12 IDATS	Illumina HT 12	-
EGAD00010000164	Affymetrix 6.0 CEL files	Affymetrix SNP 6.0	-
EGAD00010000210	Normalized expression data; discovery set	Illumina HT 12	1
EGAD00010000211	Normalized expression data; validation set	Illumina HT 12	-
EGAD00010000212	Normalized expression data; normals	Illumina HT 12	-
EGAD00010000213	Segmented (CBS) copy number aberrations (CNA); discovery set	Affymetrix SNP 6.0	-
EGAD00010000214	Segmented (CBS) copy number variants (CNV); discovery set	Affymetrix SNP 6.0	-
EGAD00010000215	Segmented (CBS) copy number aberrations (CNA); validation set	Affymetrix SNP 6.0	-
EGAD00010000216	Segmented (CBS) copy number variants (CNV); validation set	Affymetrix SNP 6.0	-
EGAD00010000217	Segmented (HMM) copy number aberrations (CNA); discovery set	Affymetrix SNP 6.0	-
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