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• W2943296176 abstract "<ns4:p><ns4:bold>Background: </ns4:bold>Ependymomas are glial tumors derived from differentiated ependymal cells. In contrast to other types of brain tumors, histological grading is not a good prognostic marker for these tumors. In order to determine genomic changes in an anaplastic ependymoma, we analyzed its mutation patterns by next generation sequencing (NGS).</ns4:p><ns4:p> <ns4:bold>Methods: </ns4:bold>Tumor DNA was sequenced using an Ion PI v3 chip on Ion Proton instrument and the data were analyzed by Ion Reporter 5.6.</ns4:p><ns4:p> <ns4:bold>Results: </ns4:bold>NGS analysis identified 19 variants, of which four were previously reported missense variants; c.395G>A in <ns4:italic>IDH1</ns4:italic>, c.1173A>G in <ns4:italic>PIK3CA</ns4:italic>, c.1416A>T in <ns4:italic>KDR</ns4:italic> and c.215C>G in <ns4:italic>TP53</ns4:italic>. The frequencies of the three missense mutations (<ns4:italic>PIK3CA</ns4:italic> c.1173A>G, <ns4:italic>KDR</ns4:italic> c.1416A>T, <ns4:italic>TP53</ns4:italic>, c.215C>G) were high, suggesting that these are germline variants, whereas the <ns4:italic>IDH1</ns4:italic> variant frequency was low (4.81%). However, based on its FATHMM score of 0.94, only the <ns4:italic>IDH1</ns4:italic> variant is pathogenic; other variants <ns4:italic>TP53</ns4:italic>, <ns4:italic>PIK3CA</ns4:italic> and <ns4:italic>KDR</ns4:italic> had FATHMM scores of 0.22, 0.56 and 0.07, respectively. Eight synonymous mutations were found in <ns4:italic>FGFR3</ns4:italic>, <ns4:italic>PDGFRA</ns4:italic>, <ns4:italic>EGFR</ns4:italic>, <ns4:italic>RET</ns4:italic>, <ns4:italic>HRAS</ns4:italic>, <ns4:italic>FLT3</ns4:italic>, <ns4:italic>APC</ns4:italic> and <ns4:italic>SMAD4</ns4:italic> genes. The mutation in <ns4:italic>FLT3</ns4:italic> p.(Val592Val) was the only novel variant found. Additionally, two known intronic variants in <ns4:italic>KDR </ns4:italic>were found and intronic variants were also found in <ns4:italic>ERBB4</ns4:italic> and <ns4:italic>PIK3CA</ns4:italic>. A known splice site mutation at an acceptor site in <ns4:italic>FLT3</ns4:italic>, a 3’-UTR variant in the <ns4:italic>CSF1R</ns4:italic> gene and a 5’_UTR variant in the <ns4:italic>SMARCB1</ns4:italic> gene were also identified. The p-values were below 0.00001 for all variants and the average coverage for all variants was around 2000x.</ns4:p><ns4:p> <ns4:bold>Conclusions: </ns4:bold>In this grade III ependymoma, one novel synonymous mutation and one deleterious missense mutation is reported. Many of the variants reported here have not been detected in ependymal tumors by NGS analysis previously and we therefore report these variants in brain tissue for the first time.</ns4:p>" @default.
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• W2943296176 date "2020-06-22" @default.
• W2943296176 modified "2023-09-27" @default.
• W2943296176 title "Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing" @default.
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• W2943296176 doi "https://doi.org/10.12688/f1000research.18721.2" @default.
• W2943296176 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/7317822" @default.
• W2943296176 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/32612806" @default.
• W2943296176 hasPublicationYear "2020" @default.
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