NBDC Research ID: hum0409.v1

 

SUMMARY

Aims: To identify genetic abnormalities that cause Exceptional Response in cancer drug therapy with VEGFR inhibitors, multi-kinase inhibitors, cytotoxic anticancer drugs, and others. Based on this information, we aim for early participation in clinical trials, acquisition of POC through off-label use, and development into investigator-initiated and corporate clinical trials.

Methods: Whole exome sequencing, Exome RNA sequencing, cfDNA target sequencing

Participants/Materials: FFPE tumor tissue DNA (13 samples) and RNA (12 samples), control normal blood cell DNA (11 samples), cell-free DNA (cfDNA) in blood (26 samples) from 11 cases of intimal sarcoma with MDM2 amplification

URL: https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000019319

 

Dataset IDType of DataCriteriaRelease Date
JGAS000619

NGS (Exome)

NGS (RNA-seq)

NGS (Target Capture)

Controlled-access (Type I) 2023/06/27

*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

intimal sarcoma with MDM2 amplification (ICD-O-3: 9137/3): 11 cases

    FFPE tumor tissue: 13 samples

    control normal blood cell: 11 samples

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [NextSeq 500]
Library Source DNAs extracted from FFPE tumor tissues and normal blood cells of patients
Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V7, SureSelect XT Reagent Kit, KAPA Hyper Prep Kit
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 75 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000748
Total Data Volume 263 GB (fastq)
Comments (Policies) NBDC policy & Cancer Research Use Only

 

RNA-seq

Participants/Materials

intimal sarcoma with MDM2 amplification (ICD-O-3: 9137/3): 10 cases

    FFPE tumor tissue: 12 samples

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [NextSeq 500]
Library Source RNAs extracted from FFPE tumor tissues
Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V7, SureSelect XT HS2 RNA Reagent Kit
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 145 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000748
Total Data Volume 110 GB (fastq)
Comments (Policies) NBDC policy & Cancer Research Use Only

 

Target Capture

Participants/Materials

intimal sarcoma with MDM2 amplification (ICD-O-3: 9137/3): 10 cases

     cell-free DNA (cfDNA) in blood: 26 samples

     control normal blood cell: 10 samples

Targets Target Capture
Target Loci for Capture Methods 737 genes
Platform Illumina [NovaSeq 6000]
Library Source cfDNA in blood and DNAs extracted from normal blood cells of patients
Cell Lines -
Library Construction (kit name) Twist Library Preparation EF Kit
Fragmentation Methods Enzymatic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Mapping Methods BWA
Mapping Quality 0≦
Reference Genome Sequence hg38
Coverage (Depth) 438x~2221x
Japanese Genotype-phenotype Archive Dataset ID JGAD000748
Total Data Volume 100 GB (bam)
Comments (Policies) NBDC policy & Cancer Research Use Only

 

DATA PROVIDER

Principal Investigator: Takafumi Koyama

Affiliation: Department of Experimental Therapeutics, National Cancer Center Hospital

Project / Group Name: NCCH1806

Funds / Grants (Research Project Number):

NameTitleProject Number
Project Promoting Clinical Trials for Development of New Drugs, Japan Agency for Medical Research and Development (AMED) Comprehensive research for clinical development and infrastructure development of super-rare cancers through the Clinical Innovation Network project of the oncology JP16lk0201044
The National Cancer Center Research and Development Fund Development of the precision liquid biopsy and evaluation of its feasibility and clinical utility 2022-A-02

 

PUBLICATIONS

TitleDOIDataset ID
1 Clinical activity and exploratory resistance mechanism of milademetan, an MDM2 inhibitor, in intimal sarcoma with MDM2 amplification doi: 10.1158/2159-8290.CD-23-0419 JGAD000748
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use