Significantly deleted CNVs included 1p35.3, 1p21.1, 3p21.2, 9p21.3, 16q21, 17q12, and 19p13.3, encompassing a great number of tumor suppressor genes, including ARID1A, MLH1, CDKN2A, CDH1, BRCA1, TP53, and SMARCA4. Based on significantly altered CNVs per sample, 70 GC patients were clustered into three subtypes by unsupervised clustering (CNV-cluster1, CNV-cluster2, and CNV-cluster3; Fig. 3E). Here, CDKN2A is linked to gastric cancer.