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| Status |
Public on Jan 31, 2024 |
| Title |
PFA ependymoma primary and recurring tumors show differences in cellularity, DNA methylation and relevant copy number variations. |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. To determine molecular differences in morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Relapsing tumors displayed a higher proportion of cell dense areas (p=0.036), a change in PF-EPN-A methylation subtypes (13/32 patients), and novel chromosome 1q gains and 6q losses (12/32 cases) compared to corresponding primary tumors.
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| Overall design |
Six pairs of posterior fossa type A ependymoma (PF-EPN-A) primary tumors and their respective first relapse were analysed, one sample per primary and relapse each. In the original study, the six cases were analysed together with additional primary relapse pairs from the CNS tumor reference cohort established by Capper et al. in 2018 [PMID: 29539639, GEO accession GSE109381] and Wenger et al. 2022 [PMID: 35842717, GEO accession GSE247880].
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| Contributor(s) |
Gödicke S, Schüller U |
| Citation(s) |
38265527 |
| Submission date |
Nov 26, 2023 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Swenja Gödicke |
| Organization name |
Research Institute Children‘s Cancer Center Hamburg
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| Lab |
Schüller
|
| Street address |
Martinistrasse 52
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| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
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| Platforms (1) |
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| Samples (12)
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| GSM7917971 |
genomic DNA from posterior fossa type A epenymoma R7 primary |
| GSM7917972 |
genomic DNA from posterior fossa type A epenymoma R7 relapse |
| GSM7917973 |
genomic DNA from posterior fossa type A epenymoma R8 primary |
| GSM7917974 |
genomic DNA from posterior fossa type A epenymoma R8 relapse |
| GSM7917975 |
genomic DNA from posterior fossa type A epenymoma R9 primary |
| GSM7917976 |
genomic DNA from posterior fossa type A epenymoma R9 relapse |
| GSM7917977 |
genomic DNA from posterior fossa type A epenymoma R10 primary |
| GSM7917978 |
genomic DNA from posterior fossa type A epenymoma R10 relapse |
| GSM7917979 |
genomic DNA from posterior fossa type A epenymoma R11 primary |
| GSM7917980 |
genomic DNA from posterior fossa type A epenymoma R11 relapse |
| GSM7917981 |
genomic DNA from posterior fossa type A epenymoma R12 primary |
| GSM7917982 |
genomic DNA from posterior fossa type A epenymoma R12 relapse |
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| This SubSeries is part of SuperSeries: |
| GSE248811 |
Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology. |
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| Relations |
| BioProject |
PRJNA1045253 |
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