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| Status |
Public on Jun 26, 2018 |
| Title |
Clinical and genetic diversity and recurrent CXorf67 mutations across distinct molecular subgroups of posterior fossa type A (PFA) ependymoma. |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
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).
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| Overall design |
The Illumina Infinium HumanMethylation450 array and IlluminaHumanMethylationEPIC (Illumina, San Diego, USA) data from n=675 patients were used to obtain genome-wide assessment of DNA methylation, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) as described previously (Pajtler et al. Cancer Cell. 2015; 27 (5), 728-743)
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| Contributor(s) |
Pajtler KW, Wen J, Sill M, Lin T, Orisme W, Ramaswamy V, Tang B, Hübner J, Dalton JD, Haupfear K, Jia S, Rogers H, Punchihewa C, Lee R, Easton J, Wu G, Chavez L, Boop FA, Klimo P, Sabin N, Ogg R, Mittag T, Jones DW, Tatevossian RG, Gajjar A, Zhang J, Taylor JP, Merchant TE, Grundy R, Taylor MD, Pfister SM, Korshunov A, Kool M, Ellison DW |
| Citation(s) |
29909548 |
| Submission date |
Sep 25, 2017 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Martin Sill |
| E-mail(s) |
m.sill@dkfz.de
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| Organization name |
DKFZ
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| Department |
Division of Pediatric Neurooncology
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platforms (2) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
| GPL21145 |
Infinium MethylationEPIC |
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| Samples (675)
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| Relations |
| BioProject |
PRJNA412037 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104210_RAW.tar |
5.7 Gb |
(http)(custom) |
TAR (of IDAT) |
| Processed data included within Sample table |
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