The CNS-GAP Project, a landmark central nervous system (CNS) disease genomics program, molecularly characterized over 4028 primary diseases and matched normal samples spanning 10 CNS types, including glioma, pituitary tumor, chordoma, medulloblastoma, medulloblastoma, vascular malformation, ependymoma, germ cell tumor, brain metastasis, brain stem tumor, and neurofibroma. The CNS-GAP has helped establish the importance of CNS diseases’ genomics, transformed our understanding of CNS diseases, and even begun to change how the disease is treated in the clinic.