Our results confirmed the previously well-defined recurrent CNVs in HCC, including recurrent gains on chr 1q21.1-q23.3 (encoding genes like BCL9, MCL1, NTRK1, DDR2, FCGR2B, and SDHC), chr 1q31.1-q44 (encoding genes like PTGS2, CDC73, IKBKE, BTG2, MDM4, PIK3C2B, USH2A, PARP1, FH, and AKT3), chr 8q21.3-q24.3 (encoding genes like NBN, RUNX1T1, CCNE2, UBR5, MYC, and RECQL4), and chr 17q22-25.3 (encoding genes like RNF43, BRIP1, CD79B, AXIN2, GNA13, PRKAR1A, SOX9, and RPTOR (as shown in Supplementary Fig S1). Here, RNF43 is linked to hepatocellular carcinoma.