NBDC Research ID: hum0111.v3

 

SUMMARY

Aims: Genomic analysis of tumor infiltrating lymphocytes in gastric cancer

Methods: RNA-seq by Illumina HiSeq 2000 and amplicon sequencing of T/B cell antigen receptors by Illumina MiSeq

Participants/Materials: Specimens of 30 diffuse-type gastric carcinoma and 60 + 15 gastric carcinoma (matched tumor and normal tissue)

 

Dataset IDType of DataCriteriaRelease Date
JGAS000103

NGS (RNA-seq)

NGS (Amplicon-seq)

Controlled-access (Type I) 2017/07/31
JGAS000141 NGS (Amplicon-seq) Controlled-access (Type I) 2019/05/31
JGAS000242 NGS (Amplicon-seq) Controlled-access (Type I) 2021/02/19

*Release Note 

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

 

MOLECULAR DATA

JGAS000103 (RNA-seq)

Participants/Materials

diffuse-type gastric carcinoma (ICD10: C16): 30 cases

(tumor tissues only)

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000]
Library Source RNAs extracted from cancer tissues from gastric carcinoma patients
Cell Lines -
Library Construction (kit name) TruSeq Stranded mRNA Sample Prep Kit
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp x 2
Japanese Genotype-phenotype Archive Dataset ID JGAD000105
Total Data Volume 5.1 MB (FPKM [txt])
Comments (Policies) NBDC policy

 

JGAS000103 (Amplicon-seq)

Participants/Materials

diffuse-type gastric carcinoma (ICD10: C16): 30 cases

(matched tumor and normal tissues)

Targets Amplicon-seq
Target Loci for Capture Methods V region to C region of TCRα, TCRβ, IgVH and IgVκ/λ genes
Platform Illumina [Miseq]
Library Source RNAs extracted from cancer and normal tissues from gastric carcinoma patients
Cell Lines -
Library Construction (kit name) Amplicon
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 300 bp x 2
Japanese Genotype-phenotype Archive Dataset ID JGAD000104
Total Data Volume 64 GB (fastq [480 files])
Comments (Policies) NBDC policy

 

JGAS000141 (Amplicon-seq)

Participants/Materials

gastric carcinoma (ICD10: C16): 60 cases

(matched tumor and normal tissues)

Targets Amplicon-seq
Target Loci for Capture Methods V region to C region of IgVH gene
Platform Illumina [Miseq]
Library Source RNAs extracted from cancer and normal tissues from gastric carcinoma patients
Cell Lines -
Library Construction (kit name) Amplicon
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 300 bp x 2
Japanese Genotype-phenotype Archive Dataset ID JGAD000210
Total Data Volume 101 GB (fastq [240 files])
Comments (Policies) NBDC policy

 

JGAS000242 (Amplicon-seq)

Participants/Materials

gastric carcinoma (ICD10: C16): 102 cases

(matched tumor and normal tissues)

(including 87 same cases in JGAD000104 and JGAD000210)

Targets Amplicon-seq
Target Loci for Capture Methods V region to C region of IgHV, IgKV and IgLV gene
Platform Illumina [Miseq]
Library Source RNAs extracted from cancer and normal tissues from gastric carcinoma patients
Cell Lines -
Library Construction (kit name) Amplicon
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 300 bp x 2
Japanese Genotype-phenotype Archive Dataset ID JGAD000342
Total Data Volume 228 GB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Shumpei Ishikawa

Affiliation: Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo

Project / Group Name: -

Funds / Grants (Research Project Number):

Name Title Project Number
KAKENHI Grant-in-Aid for Young Scientists (A) Immunogenetic Repertoire Analysis for Tumor-infiltrating Lymphocytes - toward the Understanding of Tumor Immunity - 26710009
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) Integrated genomics of cancer cells and immune cells in gastric cancer 15655817
Basic Science and Platform Technology Program for Innovative Biological Medicine, Japan Agency for Medical Research and Development (AMED) Technology development for obtaining functional and cancer-specific single-domain antigen receptor complex. JP18am0301011
Research on Development of New Drugs, Japan Agency for Medical Research and Development (AMED) Study of designing technology of high performance antibodies based on clinical genome data science and machine learning JP18ak0101096

 

PUBLICATIONS

TitleDOIDataset ID
1 Immunogenetic Profiling for Gastric Cancers Identifies Sulfated Glycosaminoglycans as Major and Functional B-cell Antigens among Human Malignancies doi: 10.1016/j.celrep.2017.07.016

JGAD000104

JGAD000105

2 Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. doi:10.1186/s12859-019-2853-y JGAD000210
3 Focal adhesion ribonucleoprotein complex proteins are major humoral cancer antigens and targets in autoimmune diseases doi: 10.1038/s42003-020-01305-5 JGAD000342

 

USERS (Controlled-access Data)

Principal Investigator: Affiliation: Data in Use (Dataset ID)Period of Data Use