Page 47 - Molecular features of low-grade developmental brain tumours

SEGA IN TSC HAVE TSC1/TSC2 BIALLELIC INACTIVATION & NO BRAF MUTATIONS
pathway with phospho-S6 ribosomal protein immunoreactivity (Figure 1F). The differential diagnosis of SEGA takes into account other tumours arising in the region of the basal ganglia and in the lateral and third ventricles (diffuse astrocytoma, ependymoma, central neurocytoma, choroid plexus papilloma). SEGA outside the setting of TSC are rare 56,57, as well as SEGA within cortical tubers 58. In our cohort, nearly all patients (n=56) had other central nervous system TSC-associated lesions (SEN and cortical tubers) associated with refractory epilepsy, making the diagnosis reasonably certain before resection.
BRAF mutational analysis
Sanger sequencing analysis for the BRAFV600E mutation in all 58 SEGA samples tested and the SEN was negative (Figure 2). Furthermore, no other variants were found in exon 15 of BRAF in any sample. We also performed RT-PCR to screen for five different types of gene fusions between KIAA1549 and BRAF on 6 SEGAs from which RNA was available (Table 2; data not shown). There was no evidence for the presence of KIAA1549-BRAF fusions in the six SEGA cases analyzed. BRAF mutational analysis was also performed by MPS for all SEGA samples for which there was sufficient DNA to permit this method of analysis, n=31 (Table 3B). None of the samples showed the BRAFV600E mutation, even at an allele frequency of 5-10%. Five intronic variants were identified, all known single nucleotide polymorphisms (SNPs; data not shown). Two coding variants in exon 1 were identified, c.82G>T (p.G28C) at allele frequency 100% in one sample, and c.31G>Ap (p.G11S) at allele frequency 56% in a second sample (Table 3B). These are not known germline variants (per Exac). The p.G11S variant has been reported in a single hepatocellular carcinoma, while the p.G28C variant has not been seen previously in cancer (per cBio). Furthermore, these two variants showed no evidence of pathogenicity based on three different in silico prediction tools.
Figure 3. Map of TSC1 and TSC2 mutations identified in 10 and 19 SEGA tumours, respectively. Novel variants (n = 9) are in blue font whereas variants previously reported (n = 16) are in black font. Circle colors present different mutation types, as indicated. A. Map of TSC1 mutations. One TSC1 mutation
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