NBDC Research ID: hum0085.v1

 

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

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000108

Array CGH

NGS (WGS)

NGS (Target Capture)

Controlled Access (Type I) 2017/10/16

*Release Note 

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MOLECULAR DATA

JGAS00000000108 (CGH)

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 Data set ID JGAD00000000116
Total Data Volume 1.55 GB (text [34 files])
Comments (Policies) NBDC policy & Cancer Research Only

 

JGAS00000000108 (WGS)

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 Data set ID JGAD00000000116
Total Data Volume 152 GB (fastq [4 files])
Comments (Policies) NBDC policy & Cancer Research Only

 

JGAS00000000108 (Target Capture)

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 Data set ID JGAD00000000116
Total Data Volume 160 GB (fastq [124 files])
Comments (Policies) NBDC policy & Cancer Research 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

TitleDOIData Set ID
1 High-density array-CGH with targeted NGS unmask multiple noncontiguous minute deletions on chromosome 3p21 in mesothelioma doi: 10.1073/pnas.1612074113 JGAD00000000116
2

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use