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 IDType of DataCriteriaRelease Date
JGAS000535

NGS (WGS)

NGS (RNA-seq)

Controlled-access (Type I) 2022/05/26

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

NGS (WGS)

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

 

NGS (RNA-seq)

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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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