SHH and chordoma: DNA methylation clustering of chordoma and extra-cranial malignant RT (MRT) and cranial atypical teratoid RT (ATRT) cases using non-negative matrix factorization (NMF; Fig. 5a, b) and uniform manifold approximation and projection (UMAP) algorithms (Fig. 5c) consistently showed that chordoma cases clustered most closely with RT subgroup 4 characterized by higher infiltration levels of cytotoxic CD8+ T cells compared to the immunologically cold ATRT-SHH and -TYR subgroups.