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Background  Genetic alterations in pediatric primary brain tumors can be used as diagnostic and prognostic markers and are the basis for the development of new target therapies that, ideally, would be associated with lower mortality and morbidity. This study evaluates the incidence and interplay of the presence of  BRAF V600E  mutation and chromosomal 9p21 deletions in a series of 100 pediatric gliomas, aiming to determine the role of these alterations in recurrence and malignant transformation, and to verify if they could be used in the clinical set for stratifying patients for tailored therapies and surveillance.    Methods  Sanger sequencing was used for the assessment of  BRAF  mutations at exon 15 and  Fluorescent  In Situ  Hybridization (FISH)  with BAC: RP11–14192 for the detection of 9p21 alterations. Expression levels of the  CDKN2A  and  MTAP  by real-time PCR were evaluated in cases with 9p21 deletions. Statistical analysis of genetic and clinical data was performed using  Graph Pad Prism 5  and  SPSS Statistics 24  software.    Results  In our cohort it was observed that 7 /78 (8,9%) of the low-grade tumors recurred and 2 (2,6%) showed malignant transformation.  BRAF V600E  mutations were detected in 15 cases. No statistically significant correlations were found between the presence of  BRAF V600E  mutation and patient’s morphologic or clinical features. Deletions at 9p21 abrogating the  CDKN2A/B  and  MTAP  loci were rare in grade I gliomas (12.2%,  p  = 0.0178) but frequent in grade IV gliomas (62.5%,  p  = 0.0087). Moreover it was found that deletions at these loci were correlated with a shorter overall survival ( p  = 0.011) and a shorter progression-free survival ( p  = 0.016).    Conclusions  It was demonstrated that in these tumors  BRAF V600E  mutated and that  CDKN2A/B MTAP  co-deletions may be used for stratifying patients for a stricter surveillance. The Investigating and defining if glial tumors with  CDKN2A/B  and  MTAP  homozygous loss may be vulnerable to new forms of therapy, namely those affecting the methionine salvage pathway, was proven to be of importance.    Electronic supplementary material  The online version of this article (10.1186/s12885-018-5120-0) contains supplementary material, which is available to authorized users.

BRAF V600E mutation and 9p21: CDKN2A/B and MTAP co-deletions - Markers in the clinical stratification of pediatric gliomas