Research ID
hum0094-v11Release info
Latest
Research title
Genomic and epigenomic analysis of different types of cancer
Research overview
- Aims
- Identification of oncogenic alteration in breast cancer, lung adenocarcinoma, colorectal cancer (CRC) and pulmonary pleomorphic carcinoma through genomic analysis. To identify new biomarkers of desmoid tumor by investigating the molecular profiles in combination with the clinicopathological characteristics.
- Methods
- Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-seq and Target Capture sequencing were performed with HiSeq 2000/2500. Methylation analysis was performed with Infinium MethylationEPIC Kit. SNP array was performed with HumanOmni2.5-8. Genomic DNA was purified from each sample; We sequenced those genomic DNAs using 10X Genomics sequencing technologies, and analyzed genomic structural variations. Long-read sequencing was performed with the Pacific Biosciences Single-Molecule Real-Time (SMRT) sequencing technology.
- Participants/materials
- Surgically resected breast cancer, lung adenocarcinoma, CRC and desmoid tumor tissues and paired non-tumor tissues or peripheral blood cells (as normal tissues)
WGS: Triple negative breast cancer: 16 cases (JGAS000095)
Lung adenocarcinoma: 7 cases (JGAS000360)
MSI-H CRC: 12 cases (JGAS000360)
Triple negative breast cancer: 11 cases (JGAS000360)
Colorectal cancer: 21 cases (JGAS000335)
WES: Triple negative breast cancer: 36 cases (including 16 cases used for WGS, 23 cases used for RNA-seq) (JGAS000095)
Lung adenocarcinoma: 43 cases (JGAS000105) + 126 cases (JGAS000215)
MSI-H CRC: 149 cases (JGAS000113)
CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 casess (JGAS000128)
Desmoid tumor: 64 cases (JGAS000270)
Pulmonary pleomorphic carcinoma: 19 cases (JGAS000297)
Colorectal cancer: 128 cases (JGAS000335)
RNA-seq: Triple negative breast cancer: 23 cases (JGAS000095)
Estrogen receptor-positive breast cancer: 17 cases (JGAS000095)
Human epidermal growth factor receptor 2 (HER2)-positive breast cancer: 15 cases (JGAS000095)
Lung adenocarcinoma: 43 cases (JGAS000105) + 126 cases (JGAS000215)
MSI-H CRC: 94 cases (JGAS000113)
CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 cases (JGAS000128)
Desmoid tumor: 55 cases (JGAS000270)
Pulmonary pleomorphic carcinoma: 33 cases (JGAS000297)
Colorectal cancer: 141 cases (JGAS000335)
Salivary duct carcinoma: 67 cases (JGAS000534)
RNA access: MSI-H CRC: 18 cases (JGAS000113)
Methylation array: MSI-H CRC: 93 cases (JGAS000113)
SNP array: MSI-H CRC: 25 cases (JGAS000113)
Target Capture: Pulmonary pleomorphic carcinoma: 20 cases (JGAS000297)
Colorectal cancer: 67 cases (JGAS000335)
Salivary duct carcinoma: 67 cases (JGAS000534)
Iso-seq: Triple negative breast cancer: 14 cases (JGAS000095)
Estrogen receptor-positive breast cancer: 8 cases (JGAS000095)
Datasets
| 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 | |
| JGAD000457 | NGS (Iso-seq, RNA-seq) |
| Controlled-access (Type I) | 2021-10-28 | |
| 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 | |
| JGAD000301 | NGS (Exome, RNA-seq) |
| Controlled-access (Type I) | 2020-10-27 | |
| JGAD000376 | NGS (Exome, RNA-seq) |
| Controlled-access (Type I) | 2021-01-26 | |
| JGAD000407 | NGS (Exome, RNA-seq, Target Capture) |
| Controlled-access (Type I) | 2021-12-22 | |
| JGAD000446 | NGS (WGS, Exome, RNA-seq, Target Capture) |
| Controlled-access (Type I) | 2022-05-17 | |
| JGAD000111 | NGS (Exome, RNA-seq) |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000653 | NGS (Target Capture, RNA-seq) |
| Controlled-access (Type I) | 2022-11-29 | |
| JGAD000474 | NGS (WGS) |
| Controlled-access (Type I) | 2021-10-12 |
Data provider
- Principal investigator
- Hiroyuki Mano
- Affiliation
- Division of Cellular Signaling, National Cancer Center Research Institute
- Principal investigator
- Shinji Kohsaka
- 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 |
|
Program for an Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED) | Establishment of infrastructure for genomic medicine and construction of knowledge database |
|
Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Implementation of precision medicine by the application of an innovative method for functional evaluation of oncogenes. |
|
Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Comprehensive exploration of biomarkers by high-throughput functional analysis for the strategic drug development |
|
Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) | Informatics for analyzing de novo human genome assemblies |
|
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 | ||
Identification of Novel CD74-NRG2α Fusion From Comprehensive Profiling of Lung Adenocarcinoma in Japanese Never or Light Smokers | ||
Comprehensive molecular and clinicopathological profiling of desmoid tumors | ||
Comprehensive molecular profiling of pulmonary pleomorphic carcinoma. | ||
Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer | ||
Exploration of predictive biomarkers for postoperative recurrence of stage II/III colorectal cancer using genomic sequencing | ||
Identification of novel prognostic and predictive biomarkers in salivary duct carcinoma via comprehensive molecular profiling |
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 |