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Background  Molecular data of histologically classified oligodendrogliomas are available offering the possibility to stratify these human brain tumors into clinically relevant molecular subtypes.    Methods  Gene copy number, mutation, and expression data of 193 histologically classified oligodendrogliomas from The Cancer Genome Atlas (TCGA) were analyzed by well-established computational approaches (unsupervised clustering, statistical testing, network inference).    Results  We applied hierarchical clustering to tumor gene copy number profiles and revealed three molecular subgroups within histologically classified oligodendrogliomas. We further screened these subgroups for molecular glioma markers (1p/19q co-deletion,  IDH  mutation, gain of chromosome 7 and loss of chromosome 10) and found that our subgroups largely resemble known molecular glioma subtypes. We excluded glioblastoma-like tumors (7a10d subgroup) and derived a gene expression signature distinguishing histologically classified oligodendrogliomas with concurrent 1p/19q co-deletion and  IDH  mutation (1p/19q subgroup) from those with predominant  IDH  mutation alone (IDHme subgroup). Interestingly, many signature genes were part of signaling pathways involved in the regulation of cell proliferation, differentiation, migration, and cell-cell contacts. We further learned a gene regulatory network associated with the gene expression signature revealing novel putative major regulators with functions in cytoskeleton remodeling (e.g.  APBB1IP ,  VAV1 ,  ARPC1B ), apoptosis ( CCNL2 ,  CREB3L1 ), and neural development (e.g.  MYTIL ,  SCRT1 ,  MEF2C ) potentially contributing to the manifestation of differences between both subgroups. Moreover, we revealed characteristic expression differences of several  HOX  and  SOX  transcription factors suggesting the activity of different glioma stemness programs in both subgroups.    Conclusions  We show that gene copy number profiles alone are sufficient to derive molecular subgroups of histologically classified oligodendrogliomas that are well-embedded into general glioma classification schemes. Moreover, our revealed novel putative major regulators and characteristic stemness signatures indicate that different developmental programs might be active in these subgroups, providing a basis for future studies.    Electronic supplementary material  The online version of this article (10.1186/s12885-018-4251-7) contains supplementary material, which is available to authorized users.

Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups