IDH1 and astrocytoma (excluding glioblastoma): For each pipeline, we observed that an 85% threshold for gene loss on chromosome arms 1p, 1q, 19p, and 19q separated all oligodendrogliomas (N = 171) from all astrocytic tumors (N = 615) in our TCGA training set, including several IDH-mutant astrocytomas that would have been considered 1p/19q-codeleted oligodendrogliomas using slightly lower thresholds (Fig. 2A, Additional file 2: Fig. 2A).