NBDC Research ID: hum0035.v1

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SUMMARY

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

Methods: We performed whole exome sequencing in 16 rhabdomyosarocoma (RMS) and 7 pleuropulmonary blastoma (PPB) patients using fresh tumors and corresponding normal blood samples. Relapsed tumor samples were also analyzed in total of 5 cases.

Participants/Materials: 16 RMSs and 7 PPBs

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

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000036 NGS (Exome) Controlled Access (Type I) 2015/09/16

*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

Participants/Materials 16 RMSs and 7 PPBs
Targets Exome
Target Loci for Capture Methods

-

Platform Illumina [HiSeq 2000/2500]
Library Source DNA extracted form 16 RMSs and 7 PPBs using fresh tumors and corresponding normal blood samples
Cell Lines -
Library Construction (kit name) SureSelect Human ALL Exon kit (50Mb kit, v4)
Fragmentation Methods 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)

Total Data Volume 523 GB (bam format)
Comments (Policies)

NBDC policy and 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

 

USERS (Controlled-Access Data)

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