NBDC Research ID: hum0035.v2

 

SUMMARY

Aims: To explore genetic alterations in solid tumors, we performed genome wide analysis using next generation sequencing methods.

Methods:

JGAS00000000036: 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.

JGAS00000000046: 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.

JGAS00000000088: 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.

Participants/Materials:

JGAS00000000036: 16 RMSs and 7 PPBs

JGAS00000000046: 522 NBs and 39 neuroblastoma cell lines

JGAS00000000088: 10 PBLs

URL: http://www.h.u-tokyo.ac.jp/vcms_lf/release_20150703.pdf

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000036 NGS (Exome) for RMS and PPB Controlled Access (Type I) 2015/09/16
JGAS00000000046

SNP-chip for NB

Target amplicon deep sequencing (NGS) for NB

Controlled Access (Type I) 2017/12/26
JGAS00000000088

SNP-chip for PBL

Methylation array for PBL

NGS (Exome) for PBL

NGS (RNA-seq) for PBL

Controlled Access (Type I) 2017/12/26

*Release Note  

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

JGAS00000000036, JGAS00000000088 (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 form 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 Data set ID

JGAD00000000036

EGAD00001000822 / EGAS00001000662 (PPB)

EGAD00001001105 / EGAS00001000884 (RMS)

JGAD00000000088

Total Data Volume 523 GB (bam format)
Comments (Policies) NBDC policy & P-DIRECT policy

 

JGAS00000000046, JGAS00000000088 (SNP-chip)

Participants/Materials

522 NBs (*sample list used in the paper)

39 neuroblastoma cell lines

10 PBLs

Targets SNP-chip
Target Loci for Capture Methods
Platform Affymetrix [GeneChip Human Mapping 250k Nspl / Cytoscan HD]
Library Source DNAs extracted form neuroblastoma cell lines, tumor tissues, and peripheral blood cells 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 Data set ID

JGAD00000000046

JGAD00000000088

Total Data Volume 35 GB (CEL)
Comments (Policies) NBDC policy & P-DIRECT policy

 

JGAS00000000046 (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 form 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 Data set ID JGAD00000000046
Total Data Volume 11 KB (xlsx [ref: hg19])
Comments (Policies) NBDC policy & P-DIRECT policy

 

JGAS00000000088 (Methylation array)

Participants/Materials 10 PBLs
Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina [Infinium MethylationEPIC]
Library Source DNAs extracted form pancreatoblastoma (tumor tissues)
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 Data set ID JGAD00000000088
Total Data Volume 110 MB (idat)
Comments (Policies) NBDC policy & P-DIRECT policy

 

JGAS00000000088 (RNA-seq)

Participants/Materials 10 PBLs
Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNAs extracted form pancreatoblastoma (tumor tissues)
Cell Lines -
Library Construction (kit name)

BioLabs NEBNext Ultra RNA Library Prep Kit for Illumina

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 Data set ID JGAD00000000088
Total Data Volume 54.8 GB (raw array data)
Comments (Policies) NBDC policy & P-DIRECT 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):

NameTitleProject Number
Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT) 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

TitleDOIData Set ID
1 Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. doi: 10.1038/ncomms8557 JGAD00000000036 EGAD00001001105
2 Biallelic DICER1 mutations in sporadic pleuropulmonary blastoma. doi: 10.1158/0008-5472.CAN-13-2470 JGAD00000000036 EGAD00001000822
3 Identification of the genetic and clinical characteristics of neuroblastomas using genome-wide analysis. doi: 10.18632/oncotarget.22495 JGAD00000000046
4 Integrated molecular characterization of the lethal pediatric cancer pancreatoblastoma. doi: 10.1158/0008-5472.CAN-17-2581 JGAD00000000088

 

USERS (Controlled-Access Data)

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