In addition to the well-known and highly recurrent events, GTS defines and ranks many previously unrecognized CNAs, uncovers frequent codeletion of two related CKI genes, CDKN2C and CDKN2A, in human cancers, and implicates APAF1 and FBXW7 in glioma pathogenesis. Here, APAF1 is linked to central nervous system cancer.