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Molecular Subgroups of Ependymoma

Source: Childhood Cancer Genomics (PDQ®)–Health Professional Version, National Cancer Institute.

Source updated: April 30, 2025 · Captured 2026-09-09.

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Context: Central Nervous System Tumors / Ependymomas

Molecular characterization studies have previously identified nine molecular subgroups of ependymoma, six of which predominate in childhood. The subgroups are determined by their distinctive DNA methylation and gene expression profiles and unique spectrum of genomic alterations (see Figure 6).[166-169]

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One new molecularly defined ependymoma was added to the 2021 World Health Organization (WHO) Classification of Tumours of the Central Nervous System: spinal ependymoma with MYCN amplification. The 2021 classification further described ependymal tumors defined by anatomical location and histology but not by molecular alteration. These tumors are called posterior fossa ependymoma (PF-EPN), supratentorial ependymoma (ST-EPN), and spinal ependymoma (SP-EPN). These tumors either contain a unique molecular alteration (not elsewhere classified [NEC]) or their molecular analysis failed or was not obtained (not otherwise specified [NOS]).[78]

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Infratentorial tumors.

Posterior fossa ependymoma (PF-EPN).

Infratentorial tumors.

Posterior fossa A (PF-EPN-A), loss of H3 K27 trimethylation mark.

Infratentorial tumors.

Posterior fossa B (PF-EPN-B), retained H3 K27 trimethylation mark.

Supratentorial tumors.

Supratentorial ependymoma (ST-EPN).

Supratentorial tumors.

ZFTA fusion–positive ependymoma (ST-EPN-ZFTA). This was previously called RELA fusion–positive ependymoma (ST-EPN-RELA), but it was renamed because ZFTA is the new designation for C11orf95, and ZFTA may be fused with a partner gene other than RELA.[170]

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Supratentorial tumors.

YAP1 fusion–positive ependymoma (ST-EPN-YAP1).

Spinal tumors.

Spinal ependymoma (SP-EPN).

Spinal tumors.

Spinal ependymoma, MYCN-amplified (SP-EPN-MYCN).

Spinal tumors.

Myxopapillary ependymoma (SP-EPN-MPE).

Subependymoma—whether supratentorial, infratentorial, or spinal—accounts for the remaining three molecular variants, and it is rarely, if ever, seen in children.

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Infratentorial tumors →Supratentorial tumors →Tumors mimicking supratentorial ependymomas →Spinal ependymoma with MYCN amplification (SP-EPN-MYCN) →

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Preserved source evidence · Independent clinical review pending · Not medical advice