A cancer genomics resource built around and driving GA4GH standards

GRIC sponsored workshop with the Swiss Institute of Bioinformatics

Michael Baudis

The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data for cancer studies. With more than 100k genomic copy number number (CNV) profiles from over 700 cancer types, Progenetix empowers comparative analyses beyond individual studies and diagnostic concepts.

Progenetix has been used in research studies, clinical diagnostics and in the development of data standards for the Global Alliance for Genomics and Health (GA4GH) and the European bioinformatics initiative ELIXIR. The Beacon+ service, implemented on top of Progenetix data, has been instrumental in developing and testing features of the Beacon protocol such as structural variant queries, “handover” data delivery and the implementation of queries for phenoptypic and diagnostic parameters for the upcoming Beacon v2 protocol. During development of GA4GH metadata concepts and schemas - which influenced standards such as the Phenopackets format - cancer specific annotations from Progenetix have informed conceptual requirements and domain-specific mappings. The resource’s focus on structural genome variants has been instrumental in addressing their specific requirements in GA4GH schema development and the Beacon protocol. In my presentation I will provide background information about GA4GH and the ELIXIR Beacon project, and how our Progenetix resource is being employed for testing GA4GH standards in a "production" environment.