For several cancer types, outcomes have improved significantly by patient stratification and individualization of treatment based on the molecular characteristics of histologically identical tumors. The potential of genomics to improve the management of distinct tumor entities is exemplified by EGFR mutant lung cancer and BRAF mutant melanoma, which can be targeted by small-molecule kinase inhibitors, as well as by the recent discovery of genetic determinants of clinical benefit from immune checkpoint blockade. It will likely be possible to extend this paradigm to other entities, protein families and classes of drugs. Advances in high-throughput DNA/RNA sequencing provide accurate information about all somatic alterations in cancer genomes at decreasing costs. However, it remains a challenge to integrate these analyses into a clinical setting. Within the NCT MASTER program, a standardized workflow including a multidisciplinary molecular tumor board was implemented and allows for tumor genome sequencing within a clinical context. These efforts may pave the way for molecularly stratified treatment trials to optimize the clinical implementation of biology-guided therapeutic interventions as well as the systematic evaluation of patient outcomes.