DAC
METABRIC data access committee
| Dac ID | Contact Person | 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 |
