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Ena-DATASET-DKFZ-IBIOS-01-08-2014-15:53:49:885-84 - samples

ABSTRACT: Whole genome bisulfite sequencing data for 6 ependymomas plus 3 fetal controls (f1, f2, f4) and 3 adult controls (a2, a3, a4). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).

PROVIDER: EGAD00001000966 | EGA |

REPOSITORIES: EGA

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Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.

Mack S C SC Witt H H Piro R M RM Gu L L Zuyderduyn S S Stütz A M AM Wang X X Wang X X Gallo M M Garzia L L Zayne K K Zhang X X Ramaswamy V V Jäger N N Jones D T W DT Sill M M Pugh T J TJ Ryzhova M M Wani K M KM Shih D J H DJ Head R R Remke M M Bailey S D SD Zichner T T Faria C C CC Barszczyk M M Stark S S Seker-Cin H H Hutter S S Johann P P Bender S S Hovestadt V V Tzaridis T T Dubuc A M AM Northcott P A PA Peacock J J Bertrand K C KC Agnihotri S S Cavalli F M G FM Clarke I I Nethery-Brokx K K Creasy C L CL Verma S K SK Koster J J Wu X X Yao Y Y Milde T T Sin-Chan P P Zuccaro J J Lau L L Pereira S S Castelo-Branco P P Hirst M M Marra M A MA Roberts S S SS Fults D D Massimi L L Cho Y J YJ Van Meter T T Grajkowska W W Lach B B Kulozik A E AE von Deimling A A Witt O O Scherer S W SW Fan X X Muraszko K M KM Kool M M Pomeroy S L SL Gupta N N Phillips J J Huang A A Tabori U U Hawkins C C Malkin D D Kongkham P N PN Weiss W A WA Jabado N N Rutka J T JT Bouffet E E Korbel J O JO Lupien M M Aldape K D KD Bader G D GD Eils R R Lichter P P Dirks P B PB Pfister S M SM Korshunov A A Taylor M D MD

Nature 20140219 7489

Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants ...[more]

PMID: 24553142

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Project description:Ependymomas are neuroepithelial tumors of the central nervous system (CNS), presenting in both adults and children but accounting for almost 10% of all pediatric CNS tumors and up to 30% of CNS tumors in children under 3 years (Bouffet et al., 2009; McGuire et al., 2009; Rodriguez et al., 2009). In children, most ependymomas arise in the posterior fossa, while most adult ependymomas present around the lower spinal cord and spinal nerve roots. Ependymomas display a wide range of morphological features, and several variants are listed in the World Health Organization (WHO) classification (Ellison et al., 2016). These variants are assigned to three WHO grades (I-III), but the clinical utility of this classification is acknowledged to be limited (Ellison et al., 2011). An increasing understanding of the genomic landscape of ependymoma and the discovery of distinct molecular groups by DNA methylation or gene expression profiling have begun to refine approaches to disease classification and prognostication, but have yet to be translated into clinical routine (Hoffman et al., 2014; Mack et al., 2014; Pajtler et al., 2017; Pajtler et al., 2015; Parker et al., 2014; Wani et al., 2012; Witt et al., 2011). Our comprehensive study of DNA methylation profiling across the entire disease demonstrated three molecular groups for each major anatomic compartment: supratentorial (ST), posterior fossa (PF), and spinal (SP) (Pajtler et al., 2015). In the ST compartment, two molecular groups (ST-EPN-RELA and ST-EPN-YAP1) align with tumors harboring specific genetic alterations, RELA and YAP1 fusion genes, which were initially discovered in a whole genome sequencing study (Parker et al., 2014). Among PF ependymomas, two of three molecular groups, PFA (PF-EPN-A) and PFB (PF-EPN-B), account for nearly all tumors; PF-SE tumors are rare, generally showing the morphology of a subependymoma (Pajtler et al., 2015). PFA tumors are found mainly in infants and young children (median age ≈ 3yrs) and have a relatively poor outcome, while PFB tumors are generally found in young adults (median age ≈ 30yrs) and are associated with a better prognosis (Pajtler et al., 2015; Witt et al., 2011). PFA tumors show few copy number alterations (CNAs), while PFB tumors harbor multiple CNAs that tend to affect entire chromosomes. While recurrent structural variants (SVs) are found in ST ependymomas, recurrent SVs or other mutations, such as single nucleotide variants (SNVs) and insertions or deletions (indels), have not been identified in PF ependymomas to date (Mack et al., 2014; Parker et al., 2014).

Dataset Information

Ena-DATASET-DKFZ-IBIOS-01-08-2014-15:53:49:885-84 - samples

Publications

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.

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