Incorporating representative genomic alterations of the three molecular subtypes ESCC1/2/3 previously identified from 90 TCGA ESCCs13 and driver genes that have been implicated in a large series of Chinese ESCCs5,32, we found that although the alteration frequencies (i.e., mutations, amplifications and deletions) of most significant genes in ESCC were similar among our subtypes, the stemness type had a higher frequency of NOTCH1 and EP300 alterations, affecting 39% and 26% of stemness tumours, respectively (Fig. 4a, Fisher’s exact test, P = 0.018 and 0.008 for NOTCH1 and EP300, respectively). This evidence concerns the gene NOTCH1 and neoplasm.