Biomarker-based translational research enables deep insight into cellular processes and human diseases. As a result, high-throughput technologies promulgating a fast and cost-effective generation of data are widely used to advance our understanding in the molecular background of individuals. However, the increasing volume and complexity of data increases the need for sustainable infrastructures and state-of-the-art tools allowing management, analysis, and integration of OMICS data. To address these challenges, we have performed site visits of core facilities with a focus on high-throughput technologies to explore their (IT) infrastructure, organizational aspects, and data management strategies. Different stakeholders were interviewed regarding requirements and needs for dealing with high-throughput data. We have identified four different fields of action: (1) the interface from biorepositories to service providers of high-throughput technologies, (2) aspects within services providers, (3) the interface from service providers to bioinformatical analysis, and (4) organizational and other aspects. For each field, recommendations and strategies were developed for implementation of a seamless pipeline from biorepositories to highly specialized high-throughput laboratories including the sustainable management and integration of OMICS data.