Fig. 2

Histopathology and results of integrative sequencing and array-based methylation profiling. Routine H&E sections showed a high-grade cellular tumor (a). Tumor cells were seen infiltrating axons (b). H3K27M stain was negative (with appropriate control staining) and H3K27me3 showed loss with expression in admixed non-neoplastic cells (c, d). Copy number profiling through MI-ONCOSEQ mainly showed whole-arm changes including gains in 1q, 7p, 17p, and losses of 13q and partial 13p (e). Gene expression (RNA-seq) showed high expression of EZHIP (CXorf67) (f, expression is presented as log-transformed fragments per kilobase of exon model per million reads mapped, or FPKM, and shown as a percentile rank among the MI-ONCOSEQ compendium). Immunohistochemistry confirmed EZHIP protein overexpression and loss of Olig2 in tumor cells (f). Reproduction of the unsupervised clustering analysis of reference and diagnostic cohorts by Capper et al. [3] using t-Distributed Stochastic Neighbor Embedding (t-SNE), with incorporation of the presented case (g). Reproduction of the Consensus Clustering analysis by Pajtler et al. [11] and incorporation of our case showing clustering with the PFA-1c subtype (h). Heatmap representation and clustering were performed identically to the previously published methods [11]. Illustration of the previously defined [11] Consensus Clustering-based PFA major subgroups and minor subtypes (n = 675) using t-SNE dimensionality reduction (i); arrowhead denotes placement of the current case. Scale bars = 40 μm