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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000103 | 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 |
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MOLECULAR DATA
| 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 |
| 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 |
| 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 |
| 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
| Title | DOI | Dataset 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 | |
| 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 |
|---|---|---|---|
