Research ID
hum0094-v4Release info
This page is a past version (v4). The latest version is v11.
Latest version (v11)Research title
Genomic and epigenomic analysis of different types of cancer
Research overview
- Aims
- Identification of oncogenic alteration in breast cancer, lung adenocarcinoma and colorectal cancer (CRC) through genomic analysis.
- Methods
- Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-seq were performed with HiSeq 2000/2500. Methylation analysis was performed with Infinium MethylationEPIC Kit. SNP array was performed with HumanOmni2.5-8.
- Participants/materials
- Surgically resected breast cancer, lung adenocarcinoma and CRC tissues and paired non-tumor tissues or peripheral blood cells (as normal tissues)
WES: Triple negative breast cancer: 36 cases (including 16 cases used for WGS and 23 cases used for RNA-seq)
Lung adenocarcinoma: 43 cases
MSI-H CRC: 149 cases
CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 casess
WGS: Triple negative breast cancer: 16 cases
RNA-seq: Triple negative breast cancer: 23 cases
Estrogen receptor-positive breast cancer: 17 cases
Human epidermal growth factor receptor 2 (HER2)-positive breast cancer: 15 cases
Lung adenocarcinoma: 43 cases
MSI-H CRC: 94 cases
CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 cases
RNA access: MSI-H CRC: 18 cases
Methylation array: MSI-H CRC: 93 cases
SNP array: MSI-H CRC: 25 cases
Datasets
The list is the one this version published; each dataset's content is shown as it is now.
| Cart | Dataset ID | Type of data | Analysis method | Access criteria | Date published |
|---|---|---|---|---|---|
| JGAD000095 | NGS (WGS, Exome, RNA-seq) |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000110 | NGS (Exome, RNA-seq) |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000122 | NGS (Exome, RNA-seq, RNA access), Methylation array, SNP array |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000139 | NGS (Exome, RNA-seq) |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000111 | NGS (Exome, RNA-seq) |
| Controlled-access (Type I) | 2020-09-28 |
Data provider
- Principal investigator
- Hiroyuki Mano
- Affiliation
- Division of Cellular Signaling, National Cancer Center Research Institute
Research projects
No research projects.
Grants
| Name | Title | Project number |
|---|---|---|
KAKENHI Grant-in-Aid for Scientific Research (C) | Oncogenic mutations of RAC small GTPases in Human cancers |
|
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Elucidation of initiation and progression mechanism of human epithelial tumors towards identification of novel therapeutic targets |
|
Leading Advanced Projects for medical innovation, The Japan Agency for Medical Research and Development (AMED) | Project for novel therapeutic targets in cancer | N/A |
Grant from The Princess Takamatsu Cancer Research Fund | Analysis of molecular mechanisms of oncogenic activity of RAC small GTPase | N/A |
Related publications
| Title | DOI | Dataset ID |
|---|---|---|
Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency | ||
Inactivating mutations and hypermethylation of the NKX2-1/TTF-1 gene in non-terminal respiratory unit-type lung adenocarcinomas. | ||
Fusion Kinases Identified by Genomic Analyses of Sporadic Microsatellite Instability-High Colorectal Cancers | ||
Genomic profiles of colorectal carcinoma with liver metastases and newly identified fusion genes |
Controlled access users
| Principal investigator | Affiliation | Country/Region | Research title | Period of data use | Dataset ID |
|---|---|---|---|---|---|
| SUBHAJYOTI DE | Rutgers Cancer Institute, Rutgers the State University of New Jersey | New Jersey, United States | Computational method development for cancer genomic data | 2018-08-06 – 2023-08-10 | |
| Youping Deng | Department of Complementary & Integrative Medicine, University of Hawaii Manoa | Hawaii, United States | Identification of driver genes and somatic mutations for lung cancer diagnosis and prognosis | 2018-10-04 – 2029-07-10 | |
| Masaki Mandai | department of Gynecology and Obstetrics, Kyoto University Faculty of Medicene | Japan | Integrated analyses of omics (genomics, transcriptomics, proteomics and metabolomics) associated with clinical variables for developing indivisualizedtreatment in gynecological malignancy | 2018-10-04 – 2025-04-14 | |
| Tetsuya Sato | Research Laboratory, H.U. Group Research Institute G.K. | Japan | Search for Lynch syndrome colorectal cancer-related genes using contolled-access clinical sequence data | 2019-08-05 – 2021-01-28 | |
| Kouya Shiraishi | Division of Genome Biology, National Cancer Research Institute | Japan | Elucidation of immune-system networks between host and tumor based on genomic analysis | 2019-08-05 – 2029-03-31 | |
| Ruping Sun | Department of laboratory medicine and pathology, University of Minnesota | Minnesota, United States | Accounting for Copy Number States in Quantifying Tumor Heterogeneity | 2020-03-19 – 2023-01-16 | |
| Masanori Arita | Bioinformation and DDBJ Center, National Institute of Genetics | Japan | Provision of processed JGA data analyzed by DDBJ Center and NBDC | 2021-10-07 – 2030-03-31 | |
| Hirofumi Nakaoka | Department of Cancer Genome Research, Sasaki Institute | Japan | Genetic analysis of lung cancer | 2022-08-17 – 2026-07-23 | |
| Michiaki Hamada | Hamada Laboratory, Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | 2023-01-05 – 2027-10-31 | |
| Nobuyuki Kakiuchi | The Hakubi Center for Advanced Research, Kyoto University | Japan | Comprehensive analysis of genetic aberrations in solid tumors | 2023-04-06 – 2028-03-31 | |
| Jin Wang | Department of Musculoskeletal Oncology, Sun Yat-sen University Cancer Center | China | Genomics study of desmoid tumor | 2023-09-06 – 2029-12-30 | |
| Charles Swanton | The Francis Crick Institute | United Kingdom | Studying lung cancer evolution in smokers and never-smokers | 2024-09-03 – 2026-05-07 | |
| Mayumi Kamada | Laboratory of Life Sciences Information Design, Department of Data Science, School of Frontier Engineering, Kitasato University | Japan | Investigation of Gene Expression Profiles in Lung Cancer: Biological Characteristics and Biomarker Development for Diagnosis and Therapy | 2025-12-08 – 2028-03-31 |