Developing adequate therapeutic options for patients affected by rare genetic disease is challenging. In addressing these challenges, a deeper understanding of the conditions beyond the levels of phenotype and genotype is crucial. This paper describes CENTOGENE’s unique data repository and how it provides not only expert understanding of rare diseases, but also enables the company to rapidly develop metabolomic-/proteomic-based biomarkers. These functional markers can facilitate patients’ diagnoses, accelerate drug development, and improve monitoring - leading to improved outcomes for patients and their care-givers.