A cancer genomics resource built on GA4GH standards

Rahel Paloots, Michael Baudis

CGC St Louis 2022

Progenetix is a cancer genomics resource that includes genomic profiling data as well as biomedical annotations and provenance data for cancer studies. The main goal of the Progenetix database is to provide easy, open access for research studies and clinical diagnostics. To facilitate sharing of genomic data, Progenetix complies with and contributes to GA4GH and Beacon data standards. Beacon, developed with the support from ELXIR (the European bioinformatics infrastructure organization), started out as protocol to share genomic variants over federated queries.

The development of Beacon (Beacon v2) enables extended metadata-rich queries in both public and restricted federated access modes. The implementation of Beacon v2 API in Progenetix offers a solution to sharing vast amounts of genomic data securely and effectively. Moreover, it represents a well-documented, open-access protcol with an open API for third party use. Currently, Progenetix contains around 130’000 cancer copy number variant (CNV) profiles from more than 700 different cancer types (NCIt classification), making it the largest publicly accessible resource for cancer CNV profiles.

In addition to primary neoplasia samples, Progenetix also includes CNV profiles from instances of several thousand cancer cell line samples. In order to provide a comprehensive cancer cell line variant database, Progenetix recently started to incorporate annotations about known single nucleotide variants of cancer cell lines, thereby laying the foundation for a comprehensive cancer cell line genomics resource, which will be instrumental in a better assignment of cancer cell lines to alteration-matched diagnostic subtypes of primary neoplasias.

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