Overall, this study detected many copy number altered peaks and important ESCC-associated driver genes such as FGFR1, PIK3CA, CCND1, CDKN2A and MRC1, which have the potential to be used as therapeutic targets in future (Du et al., 2017; Lin et al., 2014; Padhi et al., 2017; Weber et al., 2016; Weber et al., 2014). Here, CDKN2A is linked to esophageal squamous cell carcinoma.