Abstract
DNA copy number aberrations (CNAs) can be found in the majority of cancer genomes and are crucial for understanding the potential mechanisms underlying tumor initiation and progression. Since the first release in 2001, the Progenetix project (http://www.progenetix.org) has provided a reference resource dedicated to provide the most comprehensive collection of genome-wide CNA profiles. Reflecting the application of comparative genomic hybridization techniques to tens of thousands of cancer genomes, over the past 12 years our data curation efforts have resulted in a more than 60-fold increase in the number of cancer samples presented through Progenetix. In addition, new data exploration tools and visualization options have been added. In particular, the gene-specific CNA frequency analysis should facilitate the assignment of cancer genes to related cancer types. In addition, the new user file processing interface allows users to take advantage of the online tools, including various data representation options for proprietary data pre-publication. In this update article, we report recent improvements of the database in terms of content, user interface and online tools.
Highlights
DNA copy number aberrations (CNAs) are a form of genomic mutations found in the majority of individual cancer genomes [1,2,3]
According to the different substrates, Comparative genomic hybridization (CGH) platforms can be divided into chromosomal CGH and variants of array CGH [15,16,17]
We apply the term ‘array CGH (aCGH)’ broadly to cover all types of arrays resulting in whole genome copy number status data, including genomic single color arrays [e.g. single nucleotide polymorphism (SNP) arrays], for which external reference data are used
Summary
DNA copy number aberrations (CNAs) are a form of genomic mutations found in the majority of individual cancer genomes [1,2,3]. The Progenetix database represents the quantitatively largest resource for annotated CNA data from whole genome profiling experiments in cancer [35]. As a result of over 12 years of data curation, the database currently contains over 30 000 individual CNA profiles from several hundreds of cancer types.
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