EGAGenomicsInfinium HumanMethylation450 BeadChiphttps://ega-archive.org/datasets/EGAD0001000089753EGA dataset EGAD00010000897EGARhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in childhood. Here we studied 60 RMSs using whole-exome/-transcriptome sequencing, copy number (CN) and DNA methylome analyses to unravel the genetic/epigenetic basis of RMS. On the basis of methylation patterns, RMS is clustered into four distinct subtypes, which exhibits remarkable correlation with mutation/CN profiles, histological phenotypes and clinical behaviours. A1 and A2 subtypes, especially A1, largely correspond 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 are 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 the better prognosis of embryonal RMS, patients in the E2 are likely to have a poor prognosis. Our results highlight the close relationships of the methylation status and gene mutations with the biological behaviour in RMS.Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma.Seki Masafumi M, Nishimura Riki R, Yoshida Kenichi K, Shimamura Teppei T, Shiraishi Yuichi Y, Sato Yusuke Y, Kato Motohiro M, Chiba Kenichi K, Tanaka Hiroko H, Hoshino Noriko N, Nagae Genta G, Shiozawa Yusuke Y, Okuno Yusuke Y, Hosoi Hajime H, Tanaka Yukichi Y, Okita Hajime H, Miyachi Mitsuru M, Souzaki Ryota R, Taguchi Tomoaki T, Koh Katsuyoshi K, Hanada Ryoji R, Kato Keisuke K, Nomura Yuko Y, Akiyama Masaharu M, Oka Akira A, Igarashi Takashi T, Miyano Satoru S, Aburatani Hiroyuki H, Hayashi Yasuhide Y, Ogawa Seishi S, Takita Junko JfalseRMS_Infinium450KInfinium 450K in Rhabdomyosarcoma2017-07-26 15:39:26EGAD00010000897960626138366EGAC00001000207EGAS00001000884