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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000619 | Controlled-access (Type I) | 2023/06/27 |
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MOLECULAR DATA
| 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 |
| 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 |
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset 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 Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
