Cerebral
gliomas of World Health Organization (WHO) grade II and III represent a major challenge in terms of histological classification and clinical management. Here, we asked whether large-scale genomic and transcriptomic profiling improves the definition of prognostically distinct entities. We performed microarray-based genome- and transcriptome-wide analyses of primary
tumor samples from a prospective German
Glioma Network cohort of 137 patients with cerebral
gliomas, including 61 WHO grade II and 76 WHO grade III
tumors. Integrative bioinformatic analyses were employed to define molecular subgroups, which were then related to histology, molecular
biomarkers, including
isocitrate dehydrogenase 1 or 2 (IDH1/2) mutation, 1p/19q co-deletion and
telomerase reverse transcriptase (TERT) promoter mutations, and patient outcome. Genomic profiling identified five distinct
glioma groups, including three IDH1/2 mutant and two IDH1/2 wild-type groups. Expression profiling revealed evidence for eight transcriptionally different groups (five IDH1/2 mutant, three IDH1/2 wild type), which were only partially linked to the genomic groups. Correlation of
DNA-based molecular stratification with clinical outcome allowed to define three major prognostic groups with characteristic genomic aberrations. The best prognosis was found in patients with IDH1/2 mutant and 1p/19q co-deleted
tumors. Patients with IDH1/2 wild-type
gliomas and
glioblastoma-like genomic alterations, including gain on chromosome arm 7q (+7q), loss on chromosome arm 10q (-10q), TERT promoter mutation and oncogene amplification, displayed the worst outcome. Intermediate survival was seen in patients with IDH1/2 mutant, but 1p/19q intact, mostly
astrocytic gliomas, and in patients with IDH1/2 wild-type
gliomas lacking the +7q/-10q genotype and TERT promoter mutation. This molecular subgrouping stratified patients into prognostically distinct groups better than histological classification. Addition of gene expression data to this genomic classifier did not further improve prognostic stratification. In summary,
DNA-based molecular profiling of WHO grade II and III
gliomas distinguishes biologically distinct
tumor groups and provides prognostically relevant information beyond histological classification as well as IDH1/2 mutation and 1p/19q co-deletion status.