TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data

TL;DR

TRONCO is an open-source R package that infers cancer progression models from heterogeneous genomic data, aiding understanding of tumor evolution for personalized medicine.

Contribution

It provides the first comprehensive tool integrating algorithms for population and individual-level cancer progression modeling from genomic data.

Findings

Enables extraction of population-level cancer evolution trends.

Reveals clonal evolutionary history in individual patients.

Supports analysis of cross-sectional and single-cell sequencing data.

Abstract

Motivation: We introduce TRONCO (TRanslational ONCOlogy), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract population-level models describing the trends of accumulation of alterations in a cohort of cross-sectional samples, e.g., retrieved from publicly available databases, and individual-level models that reveal the clonal evolutionary history in single cancer patients, when multiple samples, e.g., multiple biopsies or single-cell sequencing data, are available. The resulting models can provide key hints in uncovering the evolutionary trajectories of cancer, especially for precision medicine or personalized therapy. Availability: TRONCO is released under the GPL license, it is hosted in the Software section at http://bimib.disco.unimib.it/ and archived also at bioconductor.org. Contact: tronco@disco.unimib.it