Integrated genetic and epigenetic analysis defines novel molecular clusters in rhabdomyosarcoma

Study ID Alternative Stable ID Type
EGAS00001000884 Other

Study Description

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in childhood. To unravel the genetic/epigenetic basis of RMS, we studied 60 RMS cases using whole exome/transcriptome sequencing, copy number (CN) profiling, and DNA methylome analysis. Based on DNA methylation patterns, RMS was clustered into 4 distinct subtypes, which exhibited remarkable correlation with mutation/CN profiles, histological phenotypes, and clinical behaviors. A1 and A2 subtypes, especially A1, largely corresponded to alveolar histology with frequent PAX3/7 fusions and alterations in cell cycle regulators. In contrast, mostly showing embryonal histology, both E1 and E2 subtypes were characterized by high frequency of CN alterations and/or allelic imbalances, FGFR4/RAS/AKT pathway mutations and PTEN mutations/methylation and in E2, also by p53 inactivation. Despite generally poor prognosis in RMS, patients in E1 cluster exceptionally showed excellent prognosis. Our results highlight the close relationship between DNA methylation status and gene mutations and biological behavior in RMS.

Study Datasets 2 datasets.

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Dataset ID Description Technology Samples
Whole-exome sequencing in 16 RMS casesWhole-transcriptome sequencing in 8 RMS cases
Illumina HiSeq 2000 38
Infinium 450K in Rhabdomyosarcoma
Infinium HumanMethylation450 BeadChip 53

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