NBDC Research ID: hum0157.v1

 

SUMMARY

Aims: Cancer clinical sequence and accompanying research for comprehensive genomic and epigenomic analyses

Methods: DNA and RNA from tumor tissues (FFPE) and DNA from normal blood cells were subjected to target capture DNA panel sequencing and RNA panel sequencing by using of NextSeq (Illumina).

Participants/Materials: 183 cancer cases (lung cancer: 53, soft tissue sarcoma: 39, colon cancer: 24, endometrial cancer: 15, ovarian cancer: 12, endometrial sarcoma: 8, hypopharyngeal cancer: 4, adenoid cystic carcinoma: 4, cancer of unknown primary: 5, other types of cancer: 19)

 

Dataset IDType of DataCriteriaRelease Date
JGAS000164 NGS (Target Capture) Controlled-access (Type I) 2019/08/19

*Release Note

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

 

MOLECULAR DATA

JGAS000164

Participants/Materials

cancer: 183 cases

(tumor tissues [FFPE sample] and normal blood cells)

     lung cancer (ICD10: C34): 53 cases

     soft tissue sarcoma (ICD10: C40-41): 39 cases

     colon cancer (ICD10: C17-20): 24 cases

     endometrial cancer (ICD10: C54): 15 cases

     ovarian cancer (ICD10: C56): 12 cases

     endometrial sarcoma (ICD10: C54): 8 cases

     hypopharyngeal cancer (ICD10: C13): 4 cases

     adenoid cystic carcinoma (ICD10: C07-08): 4 cases

     cancer of unknown primary (ICD10: D48): 5 cases

     other types of cancer: 19 cases

Targets Target Capture
Target Loci for Capture Methods

DNA panel: 464 genes

RNA panel: 449 genes

genes are listed in supplementary table 1

Platform Illumina [NextSeq]
Library Source DNAs extracted from tumor tissues and peripheral blood cells
Cell Lines -
Library Construction (kit name) SureSelectXT Custom kit
Fragmentation Methods Enzymatic Shearing (Kapa Biosystems)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 151 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000242
Total Data Volume 3 TB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Kohei Miyazono

Affiliation: Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
Program for an Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED) Establishment of infrastructure for genomic medicine and construction of knowledge database JP18kk0205003
Leading Advanced Projects for medical innovation, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-LEAP) Project for Exploration of Cancer Therapeutic Targets JP18am0001001
Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) Implementation of precision medicine by the application of an innovative method for functional evaluation of oncogenes. JP18ck0106252
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) Elucidation of initiation and progression mechanism of human epithelial tumors towards identification of novel therapeutic targets JP18cm0106502

 

PUBLICATIONS

TitleDOIDataset ID
1 Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens. doi: 10.1111/cas.13968 JGAD000242
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Hirofumi Nakaoka Department of Cancer Genome Research, Sasaki Institute Japan Genetic analysis of lung cancer JGAD000242 2022/08/06-2023/03/31