MNGO-21GENOTYPING OF MENINGIOMA BY TARGETED AMPLICON SEQUENCING USING MiSeq

Abstract

BACKGROUND: Meningiomas are the most common primary brain tumors, accounting for about 27% of all intracranial tumors. Loss of Neurofibromin 2 (NF2) is found in about half of sporadic meningiomas, and recently, mutations in TRAF7, KLF4, AKT1, and SMO are reported in non-NF2 meningioma. To establish practical genotyping methods, we performed targeted amplicon sequencing with 45 meningioma specimens and evaluated the association with clinicopathological features. METHODS: Frozen samples of 45 meningiomas were fixed with PAXgene Tissue System (QIAGEN) and embedded in paraffin (PFPE). Amplicon sequencing panel targeted NF2, TRAF7, KLF4, AKT1 and SMO were designed by GeneRead Mix-n-Match panel and Custom panel (QIAGEN). Genomic DNA was extracted from PFPE tissues and libraries were prepared using GeneRead DNAseq Targeted Panels V2 (QIAGEN). The libraries were sequenced by the MiSeq (Illumina). The raw read data obtained from amplicon sequencing were processed by GeneRead Panel Variant Calling service for analysis of mutations and copy number alterations (CNA). RESULTS: Thirty three cases (73%) harbored NF2 loss, in which 20 cases (61%) simultaneously carried NF2 mutation. Mutations in TRAF7, KLF4, AKT1, and SMO were observed in 6 (13 %), 4 (9 %), 2 (4 %) and 0 (0%) cases, respectively. Altogether, 40 of 45 case (89 %) carried at least one or more gene alteration including mutations in 5 genes listed above and NF2 loss. Result of genotyping was correlated with histological subtypes as follows. All of nine fibrous meningiomas carried NF2 loss, while all of 4 meningiomas with secretory component carried both TRAF7 and KLF4 mutations. A case of chordoid meningioma harbored only AKT1-E17K mutation. CONCLUSIONS: Here we established the clinical sequence system for meningioma by targeted amplicon sequencing with desktop sequencer in which we demonstrated favorable results for CNAs as well as mutations.