DAC Accession Contact Person Email Access Information
EGAC00000000011 Sarah_Jane Lee TDOadmin@phsa.ca http://www.ebi.ac.uk/ega/dacs/EGAC00000000011

This DAC controls 230 datasets:

Dataset Accessionsort descending Technology Samples Description
EGAD00000000045 Illumina Genome Analyzer II 1 Genomic sequencing and transcriptome shotgun sequencing of a metastatic tumour and its recurrence after drug therapy in a single patient
EGAD00000000046 Illumina Genome Analyzer II 4 RNA-SEQ data from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples
EGAD00000000047 Affymetrix 6.0 4 Signal data for from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples
EGAD00000000048 Illumina Genome Analyzer II 1 Sequencing data from oestrogen-receptor-alpha-positive metastatic lobular breast cancer sample
EGAD00000000049 Illumina Genome Analyzer II 1 RNA-SEQ data from oestrogen-receptor-alpha-positive metastatic lobular breast cancer sample
EGAD00000000114 Illumina Genome Analyzer II 1 Whole transcriptome sequence data from 18 ovarian clear-cell carcinoma samples and one TOV21G ovarian clear-cell carcinoma cell line
EGAD00001000057 Illumina Genome Analyzer II 15 RNA-Seq analysis
EGAD00001000058 Illumina Genome Analyzer II 21 Exome Sequencing analysis
EGAD00001000113 Illumina Genome Analyzer IIx, Illumina Genome Analyzer IIx; 108 Mutational landscapes of primary triple negative breast cancers - Exomes
EGAD00001000115 ABI_SOLID 32 Mutational landscapes of primary triple negative breast cancers - WGS
EGAD00001000132 Illumina Genome Analyzer IIx, Illumina Genome Analyzer IIx; 80 Mutational landscapes of primary triple negative breast cancers - RNA seq
EGAD00001000370 Illumina HiSeq 2000; 5 This dataset is compromised of 5 sequencing experiments from a single patient with sporadic and recurring parathyroid carcinoma. The samples include whole genome sequence of the primary tumor, the first recurrent tumor and peripheral blood. Whole transcriptome sequence of the first and second recurrent tumors are also included.
EGAD00001000669 Illumina Genome Analyzer; 25 High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to the emergence of treatment-resistant subclones. We sought to measure the degree of genomic diversity within primary, untreated HGSCs to examine the natural state of tumour evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on 31 spatially and temporally separated HGSC tumour specimens (six patients), including ovarian masses, distant metastases and fallopian tube lesions. We found widespread intratumoural variation in mutation, copy number and gene expression profiles, with key driver alterations in genes present in only a subset of samples (eg PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range 10.2 to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole-genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology, with common aetiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating that diversity arises at early stages of tumourigenesis. Our results revealed that HGSCs exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug-resistance mechanisms
EGAD00001000692 Illumina Genome Analyzer II;, Illumina HiSeq 2000;, Illumina Genome Analyzer; 12 Files associated with the dataset: HS1626.bam, HS1484.bam, HS1483.bam, HS1482.bam, HS1481.bam, HS1480.bam, HS1479.bam, HS1478.bam, A13805.bam, A13800.bam, A13799.bam, A05253.bam, A05252.bam, A13806.bam
EGAD00001000850 Illumina HiSeq 2000; 19 Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis.

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DAC description

Access to data generated by BCCA is made available by completing the data access agreement for review by the data access committee and will be granted to qualified investigators for appropriate use.