{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003265"],"sample_count":["70"],"description":["EGA dataset EGAD00001003265"],"repository":["EGA"],"title":["CCOC WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"description_synonyms":["Scientific Bias, Antemortem Diagnosis, chemical properties, determination, neoplasia, Blood, Xkl-1, Tumor, Diagnosis, Medical Specialties, Speciality, KL receptor activity, Gsfsco1, Specialities, Epidemiologic Biase, symptoms, SCO5, SCO1, Ecological, Polymerase Chain, preoperative procedures, Gsfsow3, Gsfsco5, SOW3, Multicase, average, Ecological Biases, thymus nucleic acid, Insurance Medicine, cell process disease, tumor disease, Sectioning, neoplasm (disease), Freeze Sectioning, Tissue, Inverse Polymerase Chain Reaction, nucleic acid library preparation, W, free, allergic reaction, medicine, malignant neoplasm, Statistical Biases, scientific observation, Reaction, Medicine, Bs, Ecological Bias, Double-Stranded DNA, Malignancies, Medicines, Systematic, tumor, deoxyribonucleic acids, DNAn, Sl, Epidemiologic Biases, Diagnose, Tumors, screening, Specialties, Anchored Polymerase Chain Reaction, chemical characterization, Scientific, Epidemiologic, Tr-kit, neoplastic disease, Double-Stranded, Ecological Fallacies, tumours, Diagnoses, (Deoxyribonucleotide)n+m, Outcome Measurement Errors, Medical Speciality, PBT, Experimental, Postmortem, Screenings, Benign, Examinations and Diagnoses, Specialty, kl1-A, simple tissue, KIT, Truncation Bias, Postmortem Diagnosis, General, desoxyribose nucleic acid, PCR, Diagnoses and Examination, tyrosine-protein kinase Kit, pbt, Postmortem Diagnoses, Bias, Nested Polymerase Chain Reaction, Review, signs, Benign Neoplasms, kit, whole genome, chemical content, Outcome Measurement, study protocol, HiSeq 2500, polymerase chain reaction, Malignant Neoplasms, Experimental Bias, Insurance Medicines, Outcome Measurement Error, Patient, Specificity and Sensitivity, PBMCs, ds DNA, Review of Reported Cases, DNA, other neoplasm, Care Standard, invasive procedures, krk1, DNS, Care Standards, (Deoxyribonucleotide)n, Ecological Fallacy, Neoplasms, Truncation, Benign Neoplasm, SCF receptor activity, Systematic Bias, Surgery, Polymerase Chain Reactions, Inverse, Malignant, Deoxyribonucleic acids, NEOPL, method, Inverse PCR, Medical Specialities, Deoxyribonucleic Acid, scfr, sensitive, PBMC, method used in an experiment, Mass, Screening, Antemortem, Medical, neoplasm, SCFR, sensitivity, Genomes., Fallacies, Fdc, Malignancy, Academic, Aggregation, nucleic acid library construction, Double Stranded, tumour, Deoxyribonucleic acid, Diagnoses and Examinations, Freeze, Neoplasias, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), drugs, Clients, Sensitivity, operative procedures, (Deoxyribonucleotide)m, Anchored PCR, Insurance, chemical structure, Neoplastic Growth, chemical composition, Cancer, Biase, Antemortem Diagnoses, measuring, Fallacy, proto-oncogene c-Kit, findings, Malignant Neoplasm, whole blood, Medical Specialty, DNAn+1, intraoperative procedures, Truncation Biases, Client, Examination and Diagnoses, neoplastic growth, Review Literature, MT, peroperative procedures, Mass Screenings, KIT ligand receptor activity, chemical analysis, Neoplasm, Errors, ds-DNA, Standards of Care, XKrk1, Anchored, c-KIT, primary cancer, Peripheral Blood, Reactions, Nested, library construction, operative therapy, Specificity, Biases, operations, patient, Cancers, CD117, disease of cellular proliferation, malignant tumor, Reticuloendothelial System, plan specification, Cryosectioning, c-kit, C-Kit, Error, Aggregation Bias, Ssm, Statistical Bias, perioperative procedures, Desoxyribonukleinsaeure, xkl-1, Nested PCR, assay, Statistical, NEOPLASMS BENIGN, Neoplasia"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-BCCA-29-03-2017-22:19:31:781-96 - samples","description":"For CCOC 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.\n\nAll CCOC 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.","dates":{"updated":"2022-11-22 12:10:03"},"accession":"EGAD00001003265","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAC00000000011","EGAS00001002390"]}}