NBDC Research ID: hum0216.v4
SUMMARY
Aims: To elucidate immune status of solid tumors including gastrointestinal cancer and to investigate tumor mutation burden for clarification of anti-tumor immuno-response.
Methods: whole exome sequencing analysis
Participants/Materials:
17 patients with lung adenocarcinomas who underwent surgery from 2015-2016
40 patients with malignancies who received PD-1 blackade therapy from 2017 to 2019
23 patients with gastric cancers who underwent surgery from 2015 to 2016
7 patients with colorectal cancer
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000216 | NGS (Exome) | Controlled-access (Type I) | 2020/02/07 |
| JGAS000244 | NGS (Exome) | Controlled-access (Type I) | 2020/09/25 |
| JGAS000216 (Data addition) | NGS (Exome) | Controlled-access (Type I) | 2021/03/29 |
| JGAS000279 | NGS (Exome) | Controlled-access (Type I) | 2021/04/13 |
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MOLECULAR DATA
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 17 cases gastric cancer (ICD10: C16): 23 cases (matched tumor and non-tumor tissues) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor or non-tumor tissues from lung adenocarcinomas and gastric cancers |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT Human All Exon system |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp x 2 |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000302 (lung adenocarcinoma) JGAD000327 (gastric cancer) |
| Total Data Volume |
JGAD000302: 230 GB (fastq) JGAD000327: 742 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
gastric cancer (ICD10: C16): 26 cases lung cancer (ICD10: C34): 9 cases malignant melanoma (ICD10: C43): 5 cases (matched tumor and non-tumor tissues) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor or non-tumor tissues from gastric cancers, lung cancers and malignant melanomas |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra DNA Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 120-150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000344 |
| Total Data Volume | 782 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
colorectal cancer (ICD10: C18.9): 7 cases (15 samples) (matched tumor and non-tumor tissues) (transverse tumor, sigmoid tumor and matched non-tumor tissues for 1 case) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor or non-tumor tissues from colorectal cancer patients |
| Cell Lines | - |
| Library Construction (kit name) |
NEBNext Ultra DNA Library Prep Kit SureSelect Human All Exon Kit v5 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000385 |
| Total Data Volume | 137 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroyoshi Nishikawa
Affiliation: Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| The National Cancer Center Research and Development Fund | Establishment of an advanced system of immune monitoring | 28-A-7 |
| The National Cancer Center Research and Development Fund | Development of novel treatment for immunotherapy-resistant cancer | 31-A-7 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Establishment of predictive methods for cancer immunotherapy based on the evaluation of cancer cells and immune responses | JP16cm0106301 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Blockade of EGFR improves responsiveness to PD1 blockade in EGFR-mutated non-small cell lung cancer | doi: 10.1126/sciimmunol.aav3937 | JGAD000302 |
| 2 | The PD-1 expression balance between effector and regulatory T cells predicts the clinical efficacy of PD-1 blockade therapies | doi: 10.1038/s41590-020-0769-3 | JGAD000344 |
| 3 | Importance of lymph node immune responses in MSI-H/dMMR colorectal cancer | doi: 10.1172/jci.insight.137365 | JGAD000385 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Takashi Kohno | Division of Genome Biology, National Cancer Center Research Institute | Identification of genetic risk factors in AYA (Adolescence and Young Adult) cancer | JGAD000302, JGAD000327, JGAD000385 | 2021/11/29-2025/03/31 | |
| Hirofumi Nakaoka | Department of Cancer Genome Research, Sasaki Institute | Japan | Genetic analysis of lung cancer | JGAD000302, JGAD000344 | 2022/08/06-2023/03/31 |
