Integrative genome analysis of the exome (27 tumours, 2 cell lines), genome (2 tumours) and transcriptome (15 tumours) of small-cell lung cancer (SCLC) has revealed a high rate of protein-changing mutations. Included amongst these mutations was inactivation of TP53 and RB1. Additionally, mutations in CREBBP, EP300 and MLL—which encode histone modifiers—were detected, as were mutations of PTEN, SLIT2 and EPHA7. These mutations might drive SCLC development and progression, representing possible targets for therapy for this aggressive cancer type.