Supratentorial Sporadic Hemangioblastoma: A Case Report With Mutation Profiling Using Next-Generation DNA Sequencing

Abstract

The present study aimed to determine genomic changes in sporadic intracranial hemangioblastoma (HBL), and the mutation patterns were analyzed using next-generation DNA sequencing (NGS). In this NGS analysis of the HBL tumor, 67 variants of 41 genes were identified. Of these, 64 were single-nucleotide variants (SNVs), two were exonic insertions and deletions (INDEL), and one was an intronic INDEL. In total, 15 were missense exonic variants, including an insertion variant in the NRAS gene, c.1_2insA, and a deletion variant, c.745delT, in the HNF1A gene, both of these mutations produced a termination codon. Other exonic missense variants found in the tumor were CTNNB1 , FGFR3 , KDR , SMO , HRAS , RAI1 , and a TP53 variant (c.430C>G). Moreover, the results of the present study revealed a novel variant, c.430C>G, in TP53 and two missense variants of SND1 (c.1810G>C and c.1814G>C), which were also novel. ALK (rs760315884) and FGFR2 (rs1042522) missense variants were reported previously. Notably, a total of 10 previously reported single-nucleotide polymorphisms (SNPs) were found in this tumor in genes including MLH1 (rs769364808), FGFR3 (rs769364808), two variants (rs1873778 and rs2228230) in PDGFRA , KIT (rs55986963), APC (rs41115), and RET (rs1800861). The results of this study revealed a synonymous mutation (SNP) in c.1104 G>T; p. (Ser368Ser) in the MLH1 gene. In this amino acid (AA) codon, two other variants are also known to cause missense substitutions, c.1103C>G; p. (Ser368Trp); COSM6986674) and c.1103C>T; p.(Ser368Leu; COSM3915870), were found in hematopoietic and urinary tract tissue, respectively. However, three SNPs found in genes such as ALK , KDR , and ABL1 in the HBL tumor in this study were not reported in UCSC, COSMIC, and ClinVar databases. Additionally, 19 intronic variants were identified in this tumor. One intronic SNV was present in each of the following genes: EGFR , ERBB4 , KDR , SMO , CDKN2B , PTEN , PTPN11 , RB1 , AKT1 , and ERBB2 . In PIK3CA and FBXL18 genes, two intronic variants were present, and in the SND1 gene, three intronic variants were detected in the HBL tumor presented in this study. Notably, only one of these was reported in the catalog of somatic mutations in canc...

Next-Generation DNA Sequencing of Grade 1 Meningioma Tumours: A Case Report of Angiomatous and Psammomatous Meningiomas

“…For example, ACP tumours exhibit activating mutations in the casein kinase-1 (CK1-alpha) and glycogen synthase kinase-3 (GSKE-3) phosphorylating domains of the CTNNB1 gene in exon 3, between amino acids 32-45, targeting the degradation of the CTNNB1 protein complex [ 29 ]. Of note, we have previously identified the PIK3CA, c.2119G>A, p. (Glu707Lys); KDR c.862T>C, p. (Phe288Leu) variants found in angiomatous meningioma in HB tumour as well [ 31 ].…”

“…Briefly, around 10 ng of DNA was used for NGS analysis, and the DNA was sequenced using an Ion PI v3 chip (Thermo Fisher Scientific) on an Ion Proton instrument sequencer Thermo Fisher Scientific). Libraries were prepared using the Ion AmpliSeq 2.0 library kit method (Thermo Fisher Scientific) and the Ion AmpliSeq cancer panel v.1 (Thermo Fisher Scientific), primer pools tagging with Ion Express barcodes (Thermo Fisher Scientific) [ 31 ]. More details of template preparation on OT2, enrichment methods, and sequencing on Ion Proton have been described previously [ 27 - 31 ].…”

“…Libraries were prepared using the Ion AmpliSeq 2.0 library kit method (Thermo Fisher Scientific) and the Ion AmpliSeq cancer panel v.1 (Thermo Fisher Scientific), primer pools tagging with Ion Express barcodes (Thermo Fisher Scientific) [ 31 ]. More details of template preparation on OT2, enrichment methods, and sequencing on Ion Proton have been described previously [ 27 - 31 ]. After the sequencing, amplicon sequences were aligned to the human reference genome GRCh37 (hg19) in the target region of cancer panel v.1 gens using the Torrent Suite software v5.10.1.0 (Thermo Fisher Scientific).…”

“…The quality assessment metrics of the chip run on an Ion Proton instrument generated by Torrent Suite software were reported by Taher et al recently [ 31 ]. In that, bead loading has been shown.…”

“…The Ion Sphere™ Particle (ISP) density image shows percentage loading across the physical surface, the final library, adapter dimers, the percentage of chip wells that contain live ISPs, total reads, usable reads, aligned and unaligned reads, total bases, key signal, and ISP summary details such as loading percentage, enrichment (polyclonal and clonal), etc. [ 31 ].…”