Cancers are genomic diseases, arising from the clonal propagation of somatic mutation events, with a limited contribution from inherited genomic variants. Genomic copy number variations are major contributors to malignant transformation and progression and constitute - at least in their quantitative extension - the largest contributors to genomic mutation landscapes, in the majority of cancer types. However, while sCNV based alterations of many canonical cancer related genes has been shown, the impact of the widespread, extensive sCNV patterns is poorly understood, not the least due to the limited amount of accessible whole-genome sCNV datasets and the lack of appropriate data standards and exchange formats. With the Progenetix and arrayMap repositories our group provides 2 of the largest resources for pre-processed CNV data in cancer, mostly based on the curation and re-analysis of data from public repositories and individual publications. As members of the Global Alliance for Genomics and Health (GA4GH) and participants in the ELIXIR h-CNV community and Beacon project, we utilise our resources to design, implement and test variant annotation and storage formats, as well as federated genome variation discovery tools such as the “Beacon” API, with focus on CNV data.