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Mutation Profiling of Intracranial Myxopapillary Ependymoma by Next Generation DNA Sequencing
Mohiuddin M Taher1,2,3, Abdulaziz Abdulnasser Alhussini3, Muhammad Saeed4
1Science and Technology Unit, Umm al Qura University, Makkah 21955, Saudi Arabia.
Objectives:
Primary intracranial myxopapillary ependymomas (MPE) are very rare. In order to determine genomic changes in an intracranial MPE, we analyzed its mutation patterns by next generation DNA sequencing.
Methods:
Tumor DNA was sequenced using an Ion PI v3 chip on Ion Proton instrument and the data were analyzed by Ion Reporter 5.6.
Results:
In this tumor, NGS generated 6,298, 354 mapped reads using the Ion PI v3 Chip. The average reads per amplicon was 29,365, 100% of amplicons had at least 500 reads and the amplicons read end-to-end were 97.58%. In this tumor, NGS data analysis identified 12 variants, of which two were missense mutations, seven were synonymous mutations and three were intronic variants. Missense mutation in c.395G>A; in exon 4 of the IDH1 gene, and a missense mutation in c.215C>G; in exon 4 of the TP53 gene were found in this tumor were previously reported. The known synonymous mutations were found in this tumor were, in exon 14 of FGFR3 in c.1953G>A; in exon 12 of PDGFRA in c.1701A>G; in exon 18 of PDGFRA c.2472C>T; in exon 20 of EGFR in c.2361G>A; in exon 13 of RET in c.2307G>T; in exon 16 of APC in c.4479G>A; and in exon 2 of MET in c.534C>T. Additionally, a known intronic variant was identified in KDR and a known acceptor site splice variant in FLT3 (rs2491231) and a SNP in the 3 ' -UTR of the CSF1R gene (rs2066934) were also identified. Except, the frequency of IDH1 variant, the frequencies of other variants were high, and the p-values were significant and Phred scores were high for all of these mutations.
Conclusions:
The variants reported in this tumor have not been detected in myxopapillary grade I ependymoma tumor by NGS analysis previously and we therefore report these variants in this case for the first time.
Insights
This study analyzed genomic alterations in a rare intracranial myxopapillary ependymoma using next-generation sequencing (NGS). We identified several novel variants, including mutations in IDH1 and TP53, providing new insights into MPE genetics.
Area of Science:
- Neuro-oncology
- Genomics
- Molecular Biology
Background:
- Primary intracranial myxopapillary ependymomas (MPE) are exceptionally rare central nervous system tumors.
- Understanding the genomic landscape of MPE is crucial for diagnosis and targeted therapy development.
Purpose of the Study:
- To identify and characterize the specific genomic alterations present in an intracranial MPE.
- To utilize next-generation DNA sequencing (NGS) for comprehensive mutation profiling of this rare tumor type.
Main Methods:
- Tumor DNA was subjected to next-generation sequencing using an Ion PI v3 chip on an Ion Proton instrument.
- Data analysis was performed using Ion Reporter 5.6 to identify genetic variants.
Main Results:
- NGS analysis yielded high-quality data with millions of mapped reads and excellent amplicon coverage.
- Twelve variants were identified, including missense mutations in IDH1 and TP53, several synonymous mutations in genes like FGFR3 and PDGFRA, and intronic/splice variants in KDR, FLT3, and CSF1R.
- Most identified variants, except for the IDH1 variant, showed high frequencies, significant p-values, and high Phred scores.
Conclusions:
- The identified variants in this intracranial MPE have not been previously reported in similar tumors via NGS analysis.
- This study reports novel genetic variants for myxopapillary ependymoma, contributing new data to the understanding of MPE molecular pathology.
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