NBDC Research ID: hum0053.v2

 

SUMMARY

Aims: Malignant pleural mesothelioma which is associated with asbestos exposure is highly aggressive and refractory to conventional therapeutic modalities. The aim of this study is identification of new targets for molecular target therapy by next generation sequencing and application of the genomic data to new diagnostic and therapeutic strategies for malignant pleural mesothelioma patients.

Methods:
Exome: We extracted genomic DNAs from surgical specimens or established mesothelioma cell lines from Japanese malignant pleural mesothelioma patients. We also extracted control DNAs from peripheral blood of the same patients. We performed whole exome sequencing using these DNAs.
WGS: We extracted genomic DNAs from established mesothelioma cell lines from Japanese malignant pleural mesothelioma patients. We sequenced those genomic DNAs using 10X Genomics sequencing technologies, and analyzed genomic structural variations.

Participants/Materials: 38 Malignant pleural mesothelioma patients (including 12 established mesothelioma cell lines)

 

Dataset IDType of DataCriteriaRelease Date
JGAS000062 NGS (Exome) Controlled-access (Type I) 2016/07/20
JGAS000176 NGS (Exome) Controlled-access (Type I) 2020/04/14

*Release Note

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

 

MOLECULAR DATA

JGAS000062

Participants/Materials

38 Malignant pleural mesothelioma patients

(38 pairs of tumor tissue and non-tumor tissue: 76 samples)

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500]
Library Source

Genomic DNAs extracted from surgical specimens or established mesothelioma cell lines from malignant pleural mesothelioma patients

Control DNAs from peripheral blood cells of the same patients

Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V4 or V5 plus lncRNA (Agilent Technologies)
Fragmentation Methods Ultrasonic fragmentation (Covaris E220)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp x 2
Japanese Genotype-phenotype Archive Dataset ID JGAD000062
Total Data Volume 596 GB (bam [76 files / ref: hg19])
Comments (Policies) NBDC policy

 

JGAS000176

Participants/Materials

12 Malignant pleural mesothelioma patients

(12 tumor tissues)

Targets WGS
Target Loci for Capture Methods -
Platform 10x Genomics [Chromium Controller]
Library Source Genomic DNAs extracted from established mesothelioma cell lines from malignant pleural mesothelioma patients
Cell Lines -
Library Construction (kit name) Chromium Genome Library & Gel Bead Kit v2
Fragmentation Methods Chromium Genome Library & Gel Bead Kit v2
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp x2
QC Methods default of 10x genomics SV-calling algorithms
Mapping Methods Long Ranger Pipeline
Depth (average) 46
Structural Variants Detection Methods Long Ranger Pipeline
Polymorphism Number (after QC) 2399
Japanese Genotype-phenotype Archive Dataset ID JGAD000256
Total Data Volume

949 GB

    Data files: 24 (fastq)

    Analysis files: 36 (vcf, bed [ref: hg38])

Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Takashi Nakano

Affiliation: Hyogo College of Medicine, Division of Respiratory Medicine

Project / Group Name: Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT)

URL: https://www.pref.aichi.jp/cancer-center/english/ri/01division/03cancer_biology/index.html

Funds / Grants (Research Project Number):

NameTitleProject Number
Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT), Japan Agency for Medical Research and Development (AMED) Development of therapeutic modalities against intractable cancers via identification of new therapeutic targets with molecular profiling (Identification of new molecular targets with profiling of malignant mesothelioma) JP15cm0106068
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) Identification of novel molecular targets by comprehensive understanding of genomic abnormalities and metabolic and cellular characteristics of malignant mesothelioma JP19cm0106606

 

PUBLICATIONS

TitleDOIDataset ID
1 Integrative molecular characterization of malignant pleural mesothelioma. doi: 10.1158/2159-8290.CD-18-0804 JGAD000062

 

USERS (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Kouya Shiraishi Division of Genome Biology, National Cancer Research Institute Elucidation of immune-system networks between host and tumor based on genomic analysis JGAD000062 2020/09/18-2023/03/31