Research ID
hum0068-v9Release info
Latest
Research title
Cancer genomics for elucidation of molecular mechanisms of carcinogenecis and progression in lung cancer
Research overview
- Aims
- Establishing a method for detecting variations of lung adenocarcinoma
- Methods
- [PCR amplicon Seq] Amplicon sequencing by using of MinION (Nanopore)
[WGS] Whole-genome sequencing for identification and characterization of a novel class of structual aberrations in cancers by using of NovaSeq and PromethION.
[RNA-seq] RNA sequencing by using of NovaSeq, HiSeq and PromethION.
[scDNA-seq] Single cell DNA sequencing by using of NovaSeq.
[Target Capture] Target capture sequencing by using of NovaSeq.
[Visium Spatial Gene Expression] Spatial transcriptome sequencing Visium (10x Genomics)
[Multiplex Fluorescence Immunostaining] Multiplex fluorescence immunostaining by PhenoCycler (Akoya Biosciences)
[Xenium In Situ Gene Expression] High-performance in situ gene expression mapping Xenium (10x Genomics) - Participants/materials
- Lung adenocarcinoma
Datasets
| Cart | Dataset ID | Type of data | Analysis method | Access criteria | Date published |
|---|---|---|---|---|---|
| JGAD000065 | NGS (PCR amplicon Seq) |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000252 | NGS (WGS: NovaSeq 6000) NGS (WGS: PromethION) |
| Controlled-access (Type I) | 2020-10-14 | |
| JGAD000696 | NGS (WGS: NovaSeq 6000) NGS (WGS: PromethION) NGS (RNA-seq : NovaSeq 6000, HiSeq 2000) NGS (Target Capture) NGS (Visium Spatial Gene Expression), Histological image Multiplex Fluorescence Immunostaining |
| Controlled-access (Type I) | 2023-02-10 | |
| JGAD000253 | NGS (WGS: NovaSeq 6000) NGS (WGS: PromethION) |
| Controlled-access (Type I) | 2020-10-14 | |
| JGAD000463 | NGS (RNA-seq: PromethION) NGS (RNA-seq: NovaSeq 6000) NGS (WGS: PromethION) |
| Controlled-access (Type I) | 2021-12-01 | |
| JGAD000807 | NGS (Visium Spatial Gene Expression), Histological image Multiplex Fluorescence Immunostaining Xenium In Situ Gene Expression |
| Controlled-access (Type I) | 2024-04-05 | |
| JGAD000670 | Processed data of JGAD000252 by JGA |
| Controlled-access (Type I) | 2023-01-19 | |
| JGAD000887 | Processed data of JGAD000252 by JGA (mitochondrial variant calls) |
| Controlled-access (Type I) | 2024-10-17 |
Data provider
- Principal investigator
- Takashi Kono
- Affiliation
- Division of Genome Biology, National Cancer Center Research Institute
Research projects
No research projects.
Grants
| Name | Title | Project number |
|---|---|---|
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Science |
|
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Conquering cancer through neo-dimensional systems understanding; Sequencing and phasing cancer mutations using a nanopore sequencer MinION |
|
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Stratification of cancer patients by novel genomic aberrations using long-read sequencing technologies |
|
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Study of genomic evolution of non-small cell lung cancers using long read sequencing technologies |
|
Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Study of heterogeneity of genomic and epigenomic aberrations and association with microenvironment in lung cancer tissues |
|
Related publications
| Title | DOI | Dataset ID |
|---|---|---|
Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer. | ||
Long-read sequencing for non-small-cell lung cancer genomes | ||
Phasing analysis of lung cancer genomes using a long read sequencer | ||
Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma |
Controlled access users
| Principal investigator | Affiliation | Country/Region | Research title | Period of data use | Dataset ID |
|---|---|---|---|---|---|
| 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 | |
| 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 | |
| Gang Fang | Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai | United States | NBDC data application | 2025-01-06 – 2029-04-01 | |
| Kenichi Yoshida | Division of Cancer Evolution, National Cancer Center Research Institute | Japan | A multicenter study on genomic analysis of solid tumors | 2024-08-01 – 2028-03-31 | |
| Hiroyuki Yasuda | Department of Pulmonary Medicine, Keio University School of Medicine | Japan | Research for biological features by gene expression analysis and biomarkers at diagnosis/therapeutics in lung cancer | 2025-05-20 – 2028-03-31 | |
| Tatsuhiro Shibata | Division of Cancer Genomics, National Cancer Center Research Institute | Japan | Study the molecular mechanics of tumor development and progression with analysing genomic mutations of liver, pancreatic, lung, gastric, colorectal, biliary tract, breast, esophageal, ovarian, cervical, bladder, renal, head-and-neck and bone cancers. | 2025-01-27 – 2026-03-31 | |
| TAKAHIRO KARASAKI | Department of Thoracic Surgery, The University of Tokyo Hospital | Japan | Development of a high-sensitivity assay for enhanced detection of circulating tumor signal | 2026-02-12 – 2030-11-30 |