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Background  The extent of intratumoral mutational heterogeneity remains unclear in gliomas, the most common primary brain tumors, especially with respect to point mutation. To address this, we applied single molecule molecular inversion probes targeting 33 cancer genes to assay both point mutations and gene amplifications within spatially distinct regions of 14 glial tumors.    Results  We find evidence of regional mutational heterogeneity in multiple tumors, including mutations in  TP53  and  RB1  in an anaplastic oligodendroglioma and amplifications in  PDGFRA  and  KIT  in two glioblastomas (GBMs). Immunohistochemistry confirms heterogeneity of  TP53  mutation and  PDGFRA  amplification. In all, 3 out of 14 glial tumors surveyed have evidence for heterogeneity for clinically relevant mutations.    Conclusions  Our results underscore the need to sample multiple regions in GBM and other glial tumors when devising personalized treatments based on genomic information, and furthermore demonstrate the importance of measuring both point mutation and copy number alteration while investigating genetic heterogeneity within cancer samples.    Electronic supplementary material  The online version of this article (doi:10.1186/s13059-014-0530-z) contains supplementary material, which is available to authorized users.

Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes