NBDC Research ID: hum0300.v1
SUMMARY
Aims: We perform integrative genome-wide analyses such as whole-exome sequencing, epigenome analysis, copy number variant (CNV) analysis, and gene expression analysis using next-generation sequencing and other methods to elucidate driver genes and signaling pathways causing tumorigenesis and cancer progression, leading novel molecular diagnostics and molecular therapies.
Methods: Whole-exome sequencing, RNA-sequencing
Participants/Materials: Whole-exome sequencing, Esophageal squamous cell carcinoma, tumor and paired non-tumor, 88 pairs; RNA-sequencing, Esophageal squamous cell carcinoma, tumor and paired non-tumor, 57 pairs
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000367 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2021/11/12 |
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MOLECULAR DATA
| Participants/Materials |
Esophageal squamous cell carcinoma (ICD10: C15): 88 cases tumor and paired non-tumor tissue |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT Human All Exon |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000481 |
| Total Data Volume | 6 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Esophageal squamous cell carcinoma (ICD10: C15): 57 cases (56 cases are also used for Exome) tumor and paired non-tumor tissue |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Ribo-Zero Magnetic Gold Kit, TruSeq Stranded mRNA Sample Prep Kit |
| Fragmentation Methods | TruSeq Stranded mRNA Sample Prep Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000481 |
| Total Data Volume | 6 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Johji Inazawa
Affiliation: Department of molecular cytogenetics, Medical Research Institute, Tokyo Medical and Dental University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Establishment of novel concept for cancer diagnostics and therapeutics based on the systematic comprehension of cellular context in cancer | 15H05908 |
| Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT), Japan Agency for Medical Research and Development (AMED) | Identification of novel therapeutic target molecules and diagnostic biomarkers for esophageal squamous cell carcinoma | JP15cm0106067 |
| Tailor-Made Medical Treatment with the BioBank Japan Project (BBJ), Japan Agency for Medical Research and Development (AMED) | Research and development for tailor-made cancer treatment based on integrative genome analyses | JP17km0506001 |
| Tokyo Medical and Dental University, Nanken-Kyoten | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrative genome-wide analyses reveal the transcriptional aberrations in Japanese esophageal squamous cell carcinoma | doi: 10.1111/cas.15063 | JGAD000481 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000481 | 2022/12/26-2025/03/31 |
| Satoshi Fujii | Department of Molecular Pathology, Yokohama City University Graduate School of Medicine | Japan | A observational study to control the accuracy of PD-L1 immunohistochemistry and to elucidate the biological significance of the staining affinity in squamous cell carcinoma across multiple organs | JGAD000481 | 2025/10/07-2026/07/22 |
