BAP1 and neoplasm: Focal amplifications in chromosome 7 harboring the MET oncogene were seen in 7 of 18 samples, while deletions were commonly seen on chromosome 3 (9/18 samples), involving VHL, SETD2, PBRM1, MLH1, and BAP1. All regions of gains and losses, with their corresponding tumor-associated genes are indicated in Additional files 8 and 9.