NBDC Research ID: hum0085.v1
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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)
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 |
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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-10] |
| Library Source | gDNA from MM tumors and reference peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Illumina TruSeq 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 |
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 |
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 |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
