108. A cancer genomics resource built on GA4GH standards

Aly Abdelkareem

Rahel Paloots

I am a PhD student at the University of Zurich, in Prof Michael Baudis group. My thesis topic is “Molecular Heterogeneity among Cancer Cell Lines and Correspondence to Primary Neoplasias”. I received my BSc from the University of Tartu, Estonia and my MSc from Ludwig-Maximilians University (LMU) in Munich.


Rahel Paloots, Michael Baudis, Hangjia Zhao, Ziying Yang

University of Zurich, Zurich, Switzerland

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 current 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 is open-access and well-documented, with an open API for third party use. Currently, Progenetix contains around 130 thousand cancer copy number variant (CNV) profiles from more than 700 different cancer types (NCIt classification), making it the largest resource for cancer CNV profiles. In addition to primary neoplasia samples, Progenetix also includes a set of cancer cell line CNV samples. In order to provide a comprehensive cancer cell line variant database, Progenetix also incorporates known single nucleotide variants of cancer cell lines.