PFA ependymoma primary and recurring tumors show differences in cellularity, DNA methylation and relevant copy number variations.

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. 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].