A cancer genomics reference resource and implementation toolkit around GA4GH standards

Q. Huang, B. Gao, R. Paloots, P. Carrio-Cordo, Z. Yang, M. Baudis

ESHG 2021

ESHG LogoThis poster presentation at the European Society of Human Genetics meeting 2021 discusses the integration and development of GA4GH standards by the Progenetix oncogenomics resource.

Abstract The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data for cancer studies. Especially through more than 100k genomic copy number number (CNV) profiles from over 500 cancer types, Progenetix empowers comparative analyses vastly exceeding 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.

We demonstrate how an open genomic reference resource has been built around emerging GA4GH standards and how it is being used to support ongoing and future developments in GA4GH and ELIXIR implementation studies, including an introduction about utilizing the Progenetix code repositories for genomics resource development. Highlights from the aggregation of cancer genomic profiling data and the associated annotations will be presented.

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2021-08-31
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