NBDC Research ID: hum0035.v3
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SUMMARY
Aims: To explore genetic alterations in solid tumors, we performed genome wide analysis using next generation sequencing methods.
Methods:
JGAS000036: Whole exome sequencing (WES) for 16 rhabdomyosarocoma (RMS) and 7 pleuropulmonary blastoma (PPB) patients using tumor tissues and corresponding normal blood cells (non-tumor tissues) were performed. Relapsed tumor tissues were also analyzed in total of 5 cases.
JGAS000046: SNP-chip analysis and targeted amplicon deep sequencing were performed using tumor tissues and corresponding normal blood cells (non-tumor tissues) from 522 neuroblastoma (NB) patients and 39 neuroblastoma cell lines.
JGAS000088: SNP-chip and WES analyses were performed using tumor tissues and corresponding normal blood cells (non-tumor tissues) from 10 pancreatoblastoma (PBL) patients. Methylation array and RNA-seq analyses were performed using only tumor tissues.
JGAS000188: SNP-chip, Methylation array, RNA-seq, and Target Capture Sequencing analyses were performed using tumor tissues from 59 hepatoblastoma (HBL) patients and 2 HBL cell lines.
Participants/Materials:
JGAS000036: 16 RMSs and 7 PPBs
JGAS000046: 522 NBs and 39 neuroblastoma cell lines
JGAS000088: 10 PBLs
JGAS000188: 59 HBLs and 2 HBL cell lines
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000036 | NGS (Exome) for RMS and PPB | Controlled-access (Type I) | 2015/09/16 |
| JGAS000046 | Controlled-access (Type I) | 2017/12/26 | |
| JGAS000088 | Controlled-access (Type I) | 2017/12/26 | |
| JGAS000188 | Controlled-access (Type I) | 2020/05/29 |
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MOLECULAR DATA
JGAS000036, JGAS000088 (Exome)
| Participants/Materials | 16 RMSs, 7 PPBs, and 10 PBLs |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNA extracted from tumor tissues and peripheral blood cells as non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human ALL Exon kit (50Mb kit, v4/v5) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75-108 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
EGAD00001000822 / EGAS00001000662 (PPB) EGAD00001001105 / EGAS00001000884 (RMS) |
| Total Data Volume |
JGAD000036: 497.04 GB (bam [ref: hg19]) JGAD000088: 179.80 GB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
JGAS000046, JGAS000088, JGAS000188 (SNP-chip)
| Participants/Materials |
522 NBs (*sample list used in the paper) 39 neuroblastoma cell lines 10 PBLs 59 HBLs and 2 HBL cell lines (ICD10: C222) |
| Targets | SNP-chip |
| Target Loci for Capture Methods | |
| Platform | Affymetrix [GeneChip Human Mapping 250k Nspl, Cytoscan HD] |
| Library Source | DNAs extracted from neuroblastoma cell lines, HBL cell lines, tumor tissues of NB and HBL, and peripheral blood cells of NB as non-tumor tissues |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix Cytoscan HD kit |
| Genotype Call Methods (software) | Copy Number for GeneChip software (CNAG) and allele-specific copy-number analysis using anonymous references (AsCNAR) |
| Marker Number |
GeneChip Human Mapping 250K Nsp Array : 262,264 CNVs CytoScan HD Array : 2,696,550 CNVs |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000046: 32.42 GB (CEL) JGAD000088: 179.80 GB (CEL) JGAD000188: 483 GB (CEL) |
| Comments (Policies) | NBDC policy |
JGAS000046 (Target amplicon deep sequencing)
| Participants/Materials | 522 NBs |
| Targets | Target Capture |
| Target Loci for Capture Methods |
159 cases (NB_001~NB_159): CHEK1, MRE11A, H2AFX, TP53, BRCA1, CHEK2, BARD1 500 cases (*see sample list): ALK, MYCN, ATRX, ARID1A, ARID1B, PHOX2B, PTPN11, HRAS, KRAS, NRAS |
| Platform | Illumina [HiSeq 2000, MiSeq] |
| Library Source | DNAs extracted from neuroblastoma (tumor tissues) |
| Cell Lines | - |
| Library Construction (kit name) | The NEBNext Ultra DNA Library Prep Kit for Illumina |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris E220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp or 150 bp |
| Mapping | BWA |
| Mutation Detection Methods | SAMtools |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000046 |
| Total Data Volume | 32.42 GB (xlsx [ref: hg19]) |
| Comments (Policies) | NBDC policy |
JGAS000088, JGAS000188 (Methylation array)
| Participants/Materials |
10 PBLs 59 HBLs and 2 HBL cell lines (ICD10: C222) |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium MethylationEPIC] |
| Library Source | DNAs extracted from tumor tissues of pancreatoblastoma and hepatoblastoma, and HBL cell lines |
| Cell Lines | - |
| Library Construction (kit name) | Infinium MethylationEPIC kit |
| Algorithms for Calculating Methylation-rate (software) | - |
| Filtering Methods | - |
| Normalization of microarray | - |
| Probe Number | 450K probes (raw data) |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000088: 179.80 GB (idat) JGAD000270: 483 GB (idat) |
| Comments (Policies) | NBDC policy |
JGAS000088, JGAS000188 (RNA-seq)
| Participants/Materials |
10 PBLs 59 HBLs and 2 HBL cell lines (ICD10: C222) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues of pancreatoblastoma and hepatoblastoma, and HBL cell lines |
| Cell Lines | - |
| Library Construction (kit name) |
NEBNext Ultra RNA Library Prep Kit for Illumina TruSeq RNA Sample Preparation Kit v2 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 108 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000088: 179.80 GB (raw array data) JGAD000270: 483 GB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 59 HBLs and 2 HBL cell lines (ICD10: C222) |
| Targets | Target Capture |
| Target Loci for Capture Methods |
380 genes or regions associated with paediatric cancers |
| Platform | Illumina [HiSeq 2000, MiSeq] |
| Library Source | DNAs extracted from tumor tissues of hepatoblastoma and HBL cell lines |
| Cell Lines | - |
| Library Construction (kit name) | The NEBNext Ultra DNA Library Prep Kit for Illumina |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris E220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp or 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000270 |
| Total Data Volume | 483 GB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Junko Takita
Affiliation: Graduate School of Medicine, The University of Tokyo
Group Name: Department of Pediatrics, Hematology/Oncology Group
Project Name: Project for Development of Innovative Research on Cancer Therapeutics -Investigation of novel molecular targets of intractable pediatric solid tumors using integrated genetic analysis-
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) | Investigation of novel molecular targets of intractable pediatric solid tumors using integrated genetic analysis | 157100000120 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Studies on clonal evolutions which regulate metastasis and relapse in pediatric solid tumors using spatiotemporal and comprehensive genome-wide analysis | 26293242 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. | doi: 10.1038/ncomms8557 | JGAD000036 EGAD00001001105 |
| 2 | Biallelic DICER1 mutations in sporadic pleuropulmonary blastoma. | doi: 10.1158/0008-5472.CAN-13-2470 | JGAD000036 EGAD00001000822 |
| 3 | Identification of the genetic and clinical characteristics of neuroblastomas using genome-wide analysis. | doi: 10.18632/oncotarget.22495 | JGAD000046 |
| 4 | Integrated molecular characterization of the lethal pediatric cancer pancreatoblastoma. | doi: 10.1158/0008-5472.CAN-17-2581 | JGAD000088 |
| 5 |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
