NBDC Research ID: hum0030.v1



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)


Data Set IDType of DataCriteriaRelease Date
JGAS00000000022 Copy Number Variations in cancer genome Controlled-Access (Type I) 2015/04/21

*Release Note

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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 Data set ID


Total Data Volume 17.5 GB
Comments (Policies)

NBDC policy & P-DIRECT policy



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):

NameTitleProject Number

KAKENHI Grant-in-Aid for Scientific Research (S)

An Integrated Genomic Analysis on Evolution of Cancer Cell Population


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


KAKENHI Grant-in-Aid for Young Scientists (B)

Search for the New Molecular Targeted Therapies Based on Genetic Profiles of Ovarian Clear Cell Carcinoma


Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT)

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)




TitleDOIData Set ID




USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Ikuo Konishi Kyoto University JGAD00000000022 2015/07/13-2017/03/31
Masaki Mandai Kyoto University Faculty of Medicene, department of Gynecology and Obstetrics JGAD00000000022 2018/10/04-2020/03/31