The literature concerning the design of large-scale high-throughput multiplexed genotyping assays for profiling tumour somatic mutations, and studies of their validation and prospective clinical use in guiding targeted therapies, is reviewed. Reports of the design and development of genotyping approaches for the simultaneous detection of numerous oncogenic driver mutations in many known cancer genes first appeared in the literature between 2007 and 2010. Retrospective studies of the detection of somatic mutations in a representative series of human tumour specimens has provided evidence of analytical validity as well as technical accuracy and reliability. Six prospective clinical studies reported since 2011 have generated evidence supporting the clinical validity of these genotyping approaches in identifying tumour somatic mutations in cancer patients in a way that could guide their treatment options. Currently, over forty different targeted drug therapies are approved for clinical use in treating cancer that therapeutically address over sixty different cancer-associated genes and hundreds of individual oncogenic driver mutations. This expanding list of targetable cancer genes and driver mutations are now candidates for inclusion in customised genotyping designs for future clinical evaluation in guiding targeted cancer therapy.