Page 48 - Molecular features of low-grade developmental brain tumours

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CHAPTER 2
(p.R509*) was seen in two different tumour samples; a large genomic deletion (deletion of exons 6-23) and a possible TSC1 mutation (c.1-7G>A) are not shown. B. map of TSC2 mutations. Two TSC2 mutations differ by a single nucleotide position in the same amino acid (p.R611Q/ p.R611W), and hence their circles overlap; one TSC2 mutation (p.R1743_K1748del) was seen in two different tumour samples.
Figure 4. Pie charts demonstrating the TSC1/TSC2 variant types and mutant allele frequencies in the SEGA tumours analyzed. A. Percentage of subjects with TSC1/TSC2 mutations identified vs. NMI. B. Different mutation types in the SEGA cohort studied.
TSC1/TSC2 mutational analysis
TSC1/TSC2 mutational analysis was performed by MPS for 34 SEGA samples (Table 3A, Figure 3 and 4). In 19 (56%) samples TSC2 mutation was identified, 10 (29%) had mutations in TSC1, and 5 (15%) had no mutation identified (NMI) in either TSC1 or TSC2. Of the 5 NMI samples 3 showed copy neutral loss of heterozygosity (CN-LOH) for TSC2 and another sample had a possible TSC1 mutation. Nine of 10 (90%) samples with a TSC1 mutation also showed evidence of CN-LOH for TSC1, 14 of 19 (74%) samples with a TSC2 mutation also showed evidence of CN-LOH for TSC2, while in 1 sample two small TSC2 mutations were identified.
Discussion
SEGAs are low-grade brain tumours associated with TSC and represent 1%-2% of all pediatric brain tumours 1,10. Due to the scarcity of resected SEGAs, studies to investigate the genetic profile of this tumour type have been restricted to a small number of samples/cases. More specifically, investigation of the presence of a BRAFV600E mutation in SEGAs has been limited to four individual studies with controversial results 18,23,26,32.
In the present study, we analyzed the largest SEGA cohort to date, consisting of fifty- eight SEGAs. Amongst the cohort the vast majority of cases (97%) were clinically diagnosed as definite TSC meeting the required criteria 33. We did not detect the cancer-actionable BRAFV600E mutation by direct sequencing or in the MPS analysis in any of the samples tested. Furthermore, there was no evidence for the presence of KIAA1549-BRAF fusions in the 6 SEGAs that were analyzed. However, no significant conclusions on BRAF fusion mutations in SEGAs could be drawn based on this small sample size (N=6). In the studies that have reported SEGA cases with BRAFV600E mutations, only two were diagnosed with definite TSC,
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