The Progenetix Project

The Progenetix database and cancer genomic information resource was publicly launched in 2001, abnnounced through an article in Bioinformatics. The resource currently contains genome profiles of more than 100’000 individual cancer genome screening experiments. The genomic profiling data was derived from array and chromosomal Comparative Genomic Hybridization (CGH) experiments as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. Genomic profiles are either processed from various raw data formats or are extracted from published experimental results.

Original diagnoses are mapped to (hierarchical) classification systems and represent several hundred different cancer types, according to the International classification of Diseases in Oncology (ICD-O) and the NCIt "neoplasm" classification, respectively. Besides genomic profiling data, Progenetix contains sample specific biological, technical and provenance information which so far has been curated from more than 1600 articles.

Access, Maintenance and Contributions

The content of the progenetix resource is freely accessible for research and commercial purposes, with attribution.

The database & software are developed by the group of Michael Baudis at the University of Zurich and the Swiss Institute of Bioinformatics [(SIB)]”.

Many previous members and external collaborators have contributed to data content and resource features. Participation (features, data, comments) by volunteers are welcome.


While we try to respond to emails in a timely manner, for requests regarding interface improvements, new use case scenarios or bug reporting we recommend to use the Github issue trackers of the progenetix-web web frontend.

Further Technical Information

Below, only publications by the Progenetix team and which directly report on Progenetix and related resources are listed here. These are usually focussed on technical aspects and content of the database, or specifically use these dataresources for large-scale metaanalyses.

For a list of publication by the Baudis group you can go to the group’s website, EuropePMC or any of the links here.

How to cite Progenetix?

@mbaudis 2021-10-12: more ...

Progenetix at GA4GH 2020 Plenary

GA4GH 8th Plenary

Michael Baudis

The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data from cancer studies. Especially through currently 113322 curated genomic copy number number (CNV) profiles from 1600 individual studies representing over 500 cancer types (NCIt), Progenetix empowers aggregate and comparative analyses which vastly exceed individual studies or single diagnostic concepts.

2020-09-30: more ...