NBDC Research ID: hum0316.v1
SUMMARY
Aims: Search for genomic mutations in esophageal squamous cell carcinoma in Japanese.
Methods: NGS libraries using DNA extracted from non-tumor tissues (normal tissues) and tumor tissues and NGS libraries using RNA extracted from tumor tissues in resected sections of esophageal squamous cell carcinoma are prepared and sequenced using Illumina HiSeq 2000/2500.
Participants/Materials: tumor tissues and non-tumor tissues of esophageal squamous cell carcinoma cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000535 | Controlled-access (Type I) | 2022/05/26 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
esophageal squamous cell carcinoma (ICD10: C15.9): 81 cases (Of these, 71 cases also underwent RNA-seq analysis) tumor tissues: 81 samples non-tumor tissues: 81 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues from esophageal squamous cell carcinoma patients |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA Sample Prep kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 125 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000654 |
| Total Data Volume | 812.3 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
esophageal squamous cell carcinoma (ICD10: C15.9): 100 cases (Of these, 71 cases also underwent WGS analysis) tumor tissues: 100 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | RNAs extracted from tumor tissues from esophageal squamous cell carcinoma patients |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA Sample Prep kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 127 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000654 |
| Total Data Volume | 812.3 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hidewaki Nakagawa
Affiliation: RIKEN Center for Integrative Medical Sciences Laboratory of Genome Sequencing Analysis
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Search for seeds for the development of novel immunotherapies and combined immunotherapies by cancer genome analysis | JP20cm0106552 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Immuno-genomic Profiling of Biopsy Specimens Predicts Neoadjuvant Chemotherapy Response in Esophageal Squamous Cell Carcinoma | doi: 10.1016/j.xcrm.2022.100705 | JGAD000654 |
| 2 |
USERS (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 | JGAD000654 | 2022/12/26-2025/03/31 |
| Shizuki Sugita | Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine | Japan | Elucidation of the impact of neoadjuvant therapy on tumor microenvironment and the factor of early recurrence in esophageal cancer patients by whole genome sequencing | JGAD000654 | 2023/03/30-2023/12/31 |
