NBDC Research ID: hum0317.v1

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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

URL: https://www.ncc.go.jp/en/ri/department/pharmacology_therapeutics/index.html

 

Dataset IDType of DataCriteriaRelease Date
JGAS000413 NGS (Exome, RNA-seq) Controlled-access (Type I) 2021/12/06

*Release Note

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

 

MOLECULAR DATA

Exome

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

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 JGAD000530
Total Data Volume 228 GB (bam [ref: hg38/mm10])
Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

Non-small cell lung cancer (ICD10: C349)

    - tumor tissues: 2 cases, 2 samples,

    - tumor tissues from PDX: 4 cases, 12 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 JGAD000530
Total Data Volume 53 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):

NameTitleProject Number
Cyclic Innovation for Clinical Empowerment, 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

 

PUBLICATIONS

TitleDOIDataset 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

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData 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