NBDC Research ID: hum0085.v2
SUMMARY
Aims: Malignant mesotheliomas (MMs) are highly aggressive adult malignancies and exposure to asbestos is the major factor involved in MM pathogenesis. It is desirable for a better understanding of the molecular pathogenesis of MM will lead to more specific and effective targeted therapies. It is reported that germline mutation in a specific gene associates familial MMs. New candidate markers to determine a subject’s predisposition to MM and for early detection need to be identified. Analysis of genomic DNA from MM tumors and reference peripheral blood cells from Japan, USA, and Turkey's patients are ongoing to find the common genomic characters beyond race.
Methods: Array CGH for chromosome 3p21, Whole Genome Sequencing (NGS), Target Capture Sequencing (NGS) and Whole Exome Sequencing (NGS)
Participants/Materials: Genomic DNA from MM tumors and reference peripheral blood cells
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000108 | Controlled-access (Type I) | 2017/10/16 | |
|
JGAS000108 (Data addition) |
Controlled-access (Type I) | 2018/09/25 |
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MOLECULAR DATA
| Participants/Materials |
MMs (ICD10: D48): total 32 cases - Japanese: 9 cases (tumors and peripheral blood cells) - American: 21 cases (tumors and peripheral blood cells), 2 cases (tumors only) |
| Targets | Array CGH |
| Target Loci for Capture Methods | 251 refseq genes on chr3p21 (Table 1) |
| Platform | The Agilent SurePrint G3 8x60K CGH Custom Microarray |
| Library Source | gDNA from MM tumors and reference peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Agilent DNA labeling kit |
| Genotype Call Methods (softwares) | Data analysis was performed using Agilent CytoGenomics 3.0.5.1. Normalization parameters were set on the GC correction (window size = 2 kb) and diploid peak centralization; the aberration detection was using algorithm ADM-2. |
| Filtering Methods | For the aberration filter, the minimum number of probes in regions was set to three and the minimum absolute average log-ratio of region was set to each array. |
| Marker Numbers (after Filtering) | Agilent Control Grid : 3886, Agilent Normalization Probe Group : 1262, Agilent Replicate Probe Group : 5000 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000116 |
| Total Data Volume | 1.55 GB (text [34 files]) |
| Comments (Policies) | NBDC policy & Cancer Research Use Only |
| Participants/Materials | MMs (ICD10: D48): 1 case (Japanese) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Library Source | gDNA from MM tumors and reference peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | IlluminaTruSeq DNA sample preparation kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000116 |
| Total Data Volume | 152 GB (fastq [4 files]) |
| Comments (Policies) | NBDC policy & Cancer Research Use Only |
| Participants/Materials |
MMs (ICD10: D48): total 31 cases - Japanese: 8 cases (tumors and peripheral blood cells) - American: 21 cases (tumors and peripheral blood cells), 2 cases (tumors only) |
| Targets | Target Capture |
| Target Loci for Capture Methods | 67 genes which were reported as candidates for MM development (chromatin remodeling, histone modification,transcription factor, TP53, CDKN2A, NF2, Table 2) |
| Platform | Illumina [MiSeq] |
| Library Source | gDNA from MM tumors and reference peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Agilent Haloplex Target Enrichment |
| Fragmentation Methods | restriction enzyme digestion |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000116 |
| Total Data Volume | 160 GB (fastq [124 files]) |
| Comments (Policies) | NBDC policy & Cancer Research Use Only |
| Participants/Materials | familial MMs (ICD10: D48): 2 cases (American) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 4000] |
| Library Source | gDNA from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Illumina SureSelect V4-post |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000116 |
| Total Data Volume | 20 GB (fastq [4 files]) |
| Comments (Policies) | NBDC policy & Cancer Research Use Only |
| Participants/Materials |
familial MMs (ICD10: D48): 38 cases (American) - Agilent Haloplex Target Enrichment & Illumina Truseq Custom Amplicon: 25 cases - Agilent Haloplex Target Enrichment only: 13 cases |
| Targets | Target Capture |
| Target Loci for Capture Methods |
Agilent Haloplex Target Enrichment: 69 genes (Table 3) Illumina Truseq Custom Amplicon: 68 genes (Table 3) |
| Platform | Illumina [MiSeq] |
| Library Source | gDNA from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Haloplex Target Enrichment, Truseq Custom Amplicon |
| Fragmentation Methods |
Agilent Haloplex Target Enrichment: restriction enzyme digestion Illumina Truseq Custom Amplicon: PCR |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Agilent Haloplex Target Enrichment: 150 bp Illumina Truseq Custom Amplicon: 250 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000116 |
| Total Data Volume | 20 GB (fastq [142 files]) |
| Comments (Policies) | NBDC policy & Cancer Research Use Only |
DATA PROVIDER
Principal Investigator: Masaki Ohmuraya
Affiliation: Department of Genetics, Hyogo College of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Deletion of the 3p region in malignant mesothelioma cells derived from Japanese patients | 24590715 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Basic research about the medical treatment based on the genomic instability of malignant mesothelioma from Japanese patients | 15K08658 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Analysis of genome structural abnormalities of 3p21 in environment-associated cancers | 25460710 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Search about germline genetic predisposition to malignant mesothelioma | 26460689 |
| Grant-in-Aid for Researchers from Hyogo College of Medicine | International collaborative research to search for the predisposition genes to malignant mesothelioma -the predisposition genes which are not confined to a particular race and asbestos exposure condition | 2015 |
| Grant-in-Aid for Researchers from Hyogo College of Medicine | Genetic variants associated with increased risk of malignant mesothelioma in Japanese. | 2017 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | High-density array-CGH with targeted NGS unmask multiple noncontiguous minute deletions on chromosome 3p21 in mesothelioma | doi: 10.1073/pnas.1612074113 | JGAD000116 |
| 2 | A Subset of Mesotheliomas With Improved Survival Occurring in Carriers of BAP1 and Other Germline Mutations | doi: 10.1200/JCO.2018.79.0352 | JGAD000116 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | 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 | JGAD000116 | 2020/09/18-2023/03/31 |
