Integrative molecular characterisation of gallbladder cancer reveals micro-environment-associated subtypes

•We profiled the mutational landscape of GBC tumours.•Aflatoxin-related signatures tended to be highly clonal.•We identified a novel TPPP-BRD9 fusion.•Poor-survival subtypes were associated with immunosuppressive micro-environments.•Tumour micro-environment could play an important role in gallbladder carcinogenesis.