This is the protocol for a series of scoping reviews that will map the general concept of methods for personalised medicine, to set the basis for the discussion on robustness and reproducibility of personalised medicine development programmes. The final goal is the identification of standards and needs in terms of methodology of data generation, management, analysis and interpretation to improve clinical studies in personalised medicine. For the purpose of this review, four main aspects of the general concept of personalised medicine will be analysed: Methods for stratification and validation cohorts Methods for machine learning applied to stratification Pre-clinical methods for translational development of treatment options and treatments selection Methods for clinical trials in personalised medicine