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 IDType of DataCriteriaRelease Date
JGAS000367 NGS (Exome, RNA-seq) Controlled-access (Type I) 2021/11/12

*Release Note

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

 

MOLECULAR DATA

Exome

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

 

RNA-seq

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):

NameTitleProject 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

TitleDOIDataset 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 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 JGAD000481 2022/12/26-2025/03/31