NBDC Research ID: hum0267.v1
SUMMARY
Aims: Pediatric solid tumors are a diverse group of neoplasms, and accurate diagnosis of tumor subtype is necessary. The detection of disease-specific fusion genes such as EWSR1-FLI1 in Ewing Sarcoma and PAX3/7-FOXO1 in alveolar rhabdomyosarcoma, can improve the diagnosis of pediatric solid tumors. In addition, recent advances in techniques have identified several subtype-defining somatic genetic alterations, including internal tandem duplication of BCOR in clear cell sarcoma of the kidney, and MYOD1 p.Leu122Arg (p.L122R) in spindle cell/sclerosing rhabdomyosarcoma. In this study, we performed transcriptome analysis using RNA-sequencing to assess its clinical utility in the differential diagnosis of pediatric solid tumors.
Methods: We performed RNA-sequencing in 47 children who suspected of sarcoma and analyzed disease-specific gene alterations (include novel gene alterations).
Participants/Materials: Forty-seven children, who were suspicious of sarcoma.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000284 | NGS (RNA-seq) | Controlled-access (Type I) | 2025/02/12 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
47 children who suspected of sarcoma (ICD10) Rhabdomyosarcoma (C499): 19, Ewing sarcoma (C419): 8, Undifferentiated sarcoma (C499): 5, Malignant rhabdoid tumor (C809): 3, Myxopapillary ependymoma (C719): 2, Clear cell sarcoma of the kidney (C64), Fetal rhabdomyomatous Nephroblastoma (C64), Inflammatory myofibroblastic tumor (-), Langerhans cell histiocytosis (C966), Liposarcoma (C499), Malignant peripheral nerve sheath tumor (C479), Neuroblastoma (C749), NUT carcinoma (C80.9), Subcutaneous panniculitis-like T-cell lymphoma (C863), Synovial sarcoma (C499): 1 case each |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra RNA Library Prep Kit for Illumina |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp x 2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000390 |
| Total Data Volume | 205.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Manabu Wakamatsu
Affiliation: Department of Pediatrics, Nagoya University Graduate School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrated diagnosis based on transcriptome analysis in suspected pediatric sarcomas | doi: 10.1038/s41525-021-00210-y | JGAD000390 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
