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
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000036 | NGS (Exome) | Controlled-access (Type I) | 2015/09/16 |
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MOLECULAR DATA
| 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 Dataset ID |
EGAD00001000822 / EGAS00001000662 (PPB) EGAD00001001105 / EGAS00001000884 (RMS) |
| Total Data Volume | 523 GB (bam format) |
| Comments (Policies) |
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 |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
| - | - | - | - |
