BAP1 and cancer: Since the Class 2 signature results from bi-allelic loss of BAP116, we inferred the temporal relationship between BAP1 loss and 15-GEP switch from Class 1 to Class 2 using the SVM discriminant score and cancer cell fraction (CCF) for BAP1 (CCFBAP1) in a subgroup of 905 cases in which copy number status was available for the BAP1 locus at chromosome 3p21.