NBDC Research ID: hum0317.v2
SUMMARY
Aims: To analyze the pharmacokinetics and therapeutic effects of anticancer drugs in patients with cancer who are undergoing or have already begun surgical resection, radiotherapy, or anticancer drug therapy by creating a patient-derived xenograft (PDX) model using patient specimens to approximate human biological tissues. This is to create a PDX model using patient specimens to analyze the pharmacokinetics and therapeutic effects of anticancer drugs in a manner that approximates human tissues.
Methods: Whole-exome sequencing and RNA-sequencing analyses
Participants/Materials:
- Non-small cell lung cancer with driver gene abnormalities 4 cases (33 samples)
- 52 cases with any cancer (germline tissues:44 samples, tumor tissues from PDX: 52 samples)
URL: https://www.ncc.go.jp/en/ri/department/pharmacology_therapeutics/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000413 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2021/12/06 |
| JGAS000707 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2024/06/20 |
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MOLECULAR DATA
| Participants/Materials |
Non-small cell lung cancer (ICD10: C349) - germline tissues: 3 cases, 3 samples - tumor tissues: 4 cases, 4 samples - tumor tissues from PDX: 4 cases, 12 samples Cancer (ICD10: C00-C97) - germline tissues: 44 cases, 44 samples - tumor tissues from PDX: 52 cases, 52 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from germline tissues, tumor tissues, and tumor tissues from PDX |
| Cell Lines | - |
| Library Construction (kit name) | Twist Comprehensive Exome Kit |
| Fragmentation Methods | Enzymatic Fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
Non-small cell lung cancer: JGAD000530 Cancer: JGAD000840 |
| Total Data Volume |
JGAD000530: 228 GB (bam [ref: hg38/mm10]) JGAD000840: 927.4 GB (bam [ref: hg38/mm10]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Non-small cell lung cancer (ICD10: C349) - tumor tissues: 2 cases, 2 samples, - tumor tissues from PDX: 4 cases, 12 samples Cancer (ICD10: C00-C97) - tumor tissues from PDX: 51 cases, 51 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from tumor tissues and tumor tissues from PDX |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra Directional RNA Library Prep Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
Non-small cell lung cancer: JGAD000530 Cancer: JGAD000840 |
| Total Data Volume |
JGAD000530: 53 GB (fastq) JGAD000840: 927.4 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Akinobu Hamada
Affiliation: Division of Molecular Pharmacology, National Cancer Center Research Institute
Project / Group Name: J-PDX library project
URL: https://www.ncc.go.jp/en/ri/department/pharmacology_therapeutics/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Cyclic Innovation for Clinical Empowerment (CiCLE), Japan Agency for Medical Research and Development (AMED) | Project to develop a PDX library derived from Japanese cancer patients for the promotion of cancer treatment | JP17pc0101011 |
| National Cancer Center Research and Development Fund | Development of a method to establish PDX that correctly reflects the diversity within human tumors | 31-A-3 |
| Research on Regulatory Science of Pharmaceuticals and Medical Devices, Japan Agency for Medical Research and Development (AMED) | Study on standardization of non-clinical studies using PDX model | JP21mk0101181 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | Establishment of PDX model for non-small cell lung cancer with genetic alteration and basic research for new drug development | 18K15296 |
| Cyclic Innovation for Clinical Empowerment (CiCLE), Japan Agency for Medical Research and Development (AMED) | Study on methods for drug discovery research to accelerate the development of anticancer drugs for rare and refractory cancers | JP20pc0101051 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Comparative study on the efficacy and exposure of molecular target agents in non-small cell lung cancer PDX models with driver genetic alterations | doi: 10.1158/1535-7163.MCT-21-0371 | JGAD000530 |
| 2 | A molecular glue RBM39-degrader induces synthetic lethality in cancer cells with homologous recombination repair deficiency | doi: 10.1038/s41698-024-00610-0 | JGAD000840 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Hirofumi Nakaoka | Department of Cancer Genome Research, Sasaki Institute | Japan | Genetic analysis of lung cancer | JGAD000530 | 2022/08/06-2023/03/31 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000530 | 2022/12/26-2025/03/31 |
