NBDC Research ID: hum0030.v1
SUMMARY
Aims: To clarify the molecular biological difference between ovarian clear cell carcinoma and other histological subtypes carcinomas by comparing the copy number variants.
Methods: Gene Chip Human Mapping 250K Nsp Arrays were used for detecting the signal intensity of about 260 thousands SNPs and intensities of ovarian clear cell carcinoma were compared to the ones of non-carcinoma.
Participants/Materials: 57 ovarian carcinoma patients (ovarian cancer cells and peripheral blood cells: total 114 samples)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000022 | Copy Number Variations in cancer genome | Controlled-access (Type I) | 2015/04/21 |
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MOLECULAR DATA
| Participants/Materials: |
Surgical samples were obtained from 57 patients (31 clear cell carcinomas, 14 serous adenocarcinomas, and 12 endometrioid adenocarcinomas) |
| Targets | genome wide CNVs |
| Target Loci for Capture Methods |
- |
| Platform | Affymetrix [GeneChip Human Mapping 250K Nsp Array] |
| Source | gDNAs extracted from ovarian cancer cells and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | GeneChip Human Mapping 250K Nsp Array |
| Algorithm for detecting CNVs (software) | genome imbalance map (GIM) algorithm (doi:10.1016/j.bbrc.2005.06.040) |
| CNV number | 262,264 CNVs |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume | 17.5 GB |
| Comments (Policies) |
DATA PROVIDER
Principal Investigator: Katsutoshi Oda
Affiliation: Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (S) | An Integrated Genomic Analysis on Evolution of Cancer Cell Population | 24221011 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Search for the New Molecular Targeted Therapies and Biomarkers Inducing Apoptosis in Endometrial Carcinoma and Ovarian Carcinoma | 26462515 |
| KAKENHI Grant-in-Aid for Young Scientists (B) | Search for the New Molecular Targeted Therapies Based on Genetic Profiles of Ovarian Clear Cell Carcinoma | 25861473 |
| Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT), Japan Agency for Medical Research and Development (AMED) | Development of the Intractable Cancer Therapies through the New Target Identification by the Molecular Profiling (The Identification of the Gene Variation to Regulate the Treatment Sensitivity of the Progressive Ovarian Cancer) | 11114014 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrated Copy Number and Expression Analysis Identifies Profiles of Whole-Arm Chromosomal Alterations and Subgroups with Favorable Outcome in Ovarian Clear Cell Carcinomas | doi: 10.1371/journal.pone.0128066 | JGAD000022 |
| 2 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
| Ikuo Konishi | Kyoto University | JGAD000022 | 2015/07/13-2017/03/31 | |
| Masaki Mandai | Kyoto University Faculty of Medicene, department of Gynecology and Obstetrics | Integrated analyses of omics (genomics, transcriptomics, proteomics and metabolomics) associated with clinical variables for developing indivisualizedtreatment in gynecological malignancy | JGAD000022 | 2018/10/04-2025/03/31 |
