ATE1 and neoplasm: EMT tumor 222 had a similarly bounded focal amplification event over FGFR2 and ATE1 that increased both gene copy numbers by 1, but EMT tumor 1356 has an estimated copy number gain of 471 over this region and correlates well with gene expression levels of FGFR2 (Additional files 26 and 28: Tables S1 and S3).