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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000062 | NGS (Exome) | Controlled-access (Type I) | 2016/07/20 |
| JGAS000176 | NGS (Exome) | Controlled-access (Type I) | 2020/04/14 |
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MOLECULAR DATA
| 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 |
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrative molecular characterization of malignant pleural mesothelioma. | doi: 10.1158/2159-8290.CD-18-0804 | JGAD000062 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data 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 |
