NBDC Research ID: hum0327.v1
SUMMARY
Aims: Cancers in the hepatobiliary and pancreatic regions are not only common but also difficult to cure. Recently, it has been reported that mutant peptides newly generated by genetic mutations are recognized by the immune system as neoantigens, and the development of immunotherapy targeting these peptides has been promoted. In this study, in order to develop effective immunotherapy for hepatobiliary and pancreatic cancers and to propose it as a new cancer therapy, we will first identify different genetic mutations and antigens in each patient with these cancers, and then verify the practicality of immunotherapy using a diverse population of T cells that recognize them.
Methods: Paired fresh normal and tumor tissues were collected from surgically resected HCC and mCRC. RNA and genomic DNA were extracted from tumor/normal tissues (2–5 mm in diameter) and used for whole exome sequencing or RNA sequencing with NextSeq 550 (Illumina).
Participants/Materials: Tumor tissues were collected from liver cancer patients, who were received surgical resection at the National Cancer Center Hospital East (NCCE) between 2017 and 2020.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000507 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2022/02/25 |
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MOLECULAR DATA
| Participants/Materials |
hepatocellular carcinoma (ICD10: C22.0): 28 cases metastatic colorectal carcinoma (ICD10: C22.7): 18 cases tumor and paired non-tumor tissues |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 550] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT library preparation kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000624 |
| Total Data Volume | 1.0 TB (fastq, vcf) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hepatocellular carcinoma (ICD10: C22.0): 28 cases metastatic colorectal carcinoma (ICD10: C22.7): 18 cases tumor and paired non-tumor tissues |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 550] |
| Library Source | RNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA Library prep kit, SureSelect strand specific RNA |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000624 |
| Total Data Volume | 1.0 TB (fastq, tpm) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshihiro Suzuki
Affiliation: Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center
Project / Group Name: Development of personalize neoantigen vaccine
URL： https://www.ncc.go.jp/en/epoc/division/immunotherapy/kashiwa/030/020/20170728190117.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Collaboration funding from BrightPath Biotherapeutics Co., Ltd. | Development of the methodology for individualized neoantigen vaccine therapy | C2017-054 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Development of antigen-prediction algorithm for personalized neoantigens vaccine using human leukocyte antigen transgenic mouse. | doi: 10.1111/cas.15291 | JGAD000624 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data 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 | JGAD000624 | 2022/12/26-2025/03/31 |
