Mutation profiling of Anaplastic Ependymoma Grade III by Ion Proton Next Generation DNA Sequencing

Ependymomas are glial tumors derived from differentiated ependymal cells lining the ventricles, in contrast to other types of brain tumors, histological grading is not a good prognostic marker for outcome for these tumors. In order to determine the genomic changes in anaplastic ependymoma, we have analyzed by Next generation DNA sequencing the mutation patterns in this tumor. NGS data analysis identified 19 variants, out of which four were previously reported, viz., in IDH1 gene a known missense mutation c.395G>A, a missense variant PIK3CA, c.1173A>G; in KDR c.1416A>T; in TP53 a mutation in c.215C>G were found respectively. The frequencies of the three missense mutations were high suggesting these are germ line variants, whereas IDH1 variant frequency was low (4.81%). Only variants in TP53, PIK3CA, IDH1, and KDR have the positive PolyPhen2 score. However, only IDH1 variant detected in this tumor is a pathogenic one. Eight synonymous mutations found in this tumor were, in FGFR3, PDGFRA, EGFR, RET, HRAS, FLT3, APC, and in SMAD4 genes respectively. The synonymous mutation in FLT3 p. (Val592Val) is only a novel variant one found. Also, two known intronic variants in KDR a known splice site mutation at acceptor site in FLT3, and a 3’-UTR variant in CSF1R gene were identified. Additionally, in SMARCB1 a 5’_UTR variant, and an intronic variant in ERBB4 and PIK3CA respectively were found. The p-value and Phred score were significantly high for all these mutations, and the sequencing quality and coverage details of all mutations also presented here. In conclusion, in the grade III ependymoma, only one mutation (synonymous) was novel, and only one missense mutation is deleterious. Many of the variants we reported here were not detected in the ependymal tumors by NGS analysis previously, and we report many of these variants in the brain tissue for the first time.