Single-nucleotide variants (SNVs)/insertion and deletions (Indels) in 11 genes were frequently identified in MBC (ESR1, SMARCA4, NF1, FGFR4, ARID2, PARP1, TSC2, ATRX, ARID1A, AURKA, and STAG2 at false discovery rate [FDR] < 5%) compared with those in PBC, and ESR1 amplifications were frequently identified in MBC samples (Fig. 2a–b and Supplementary Table 8). Here, STAG2 is linked to primary biliary cholangitis.