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GCT WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

For GCT cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All GCT tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

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BC Cancer, part of the Provincial Health Services Authority - Data Access Policy

Access to this data is controlled. There are a number of steps that a researcher must take to obtain access to this data, including execution of a Data Access Agreement between the institutions. The process is overseen by the Technology Development Office; please contact our general email address TDOadmin@phsa.ca. Please only click the "request data" button on the EGA website after a Data Access Agreement is fully executed.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001002390 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00001589678 bam 76.2 GB
EGAF00001589679 bam 76.6 GB
EGAF00001589680 bam 71.4 GB
EGAF00001589681 bam 72.6 GB
EGAF00001589682 bam 72.3 GB
EGAF00001589683 bam 69.8 GB
EGAF00001589684 bam 71.1 GB
EGAF00001589685 bam 78.1 GB
EGAF00001589686 bam 70.6 GB
EGAF00001589687 bam 72.3 GB
EGAF00001589811 bam 110.6 GB
EGAF00001589812 bam 126.3 GB
EGAF00001589813 bam 118.9 GB
EGAF00001589814 bam 129.9 GB
EGAF00001589815 bam 134.4 GB
EGAF00001589816 bam 103.9 GB
EGAF00001589817 bam 113.9 GB
EGAF00001589818 bam 127.5 GB
EGAF00001589819 bam 115.2 GB
EGAF00001589820 bam 113.2 GB
20 Files (1.9 TB)