Journal Article

LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution

Angaroni, Fabrizio, Bhavesh, Narra Lakshmi Sai, Craighero, Francesco, Damiani, Chiara, Ascolani, Gianluca, Maspero, Davide, Antoniotti, Marco, Piazza, Rocco, Ramazzotti, Daniele, Graudenzi, Alex

2023

Overview

Background Longitudinal single-cell sequencing experiments of patient-derived models are increasingly employed to investigate cancer evolution. In this context, robust computational methods are needed to properly exploit the mutational profiles of single cells generated via variant calling, in order to reconstruct the evolutionary history of a tumor and characterize the impact of therapeutic strategies, such as the administration of drugs. To this end, we have recently developed the LACE framework for the Longitudinal Analysis of Cancer Evolution. Results The LACE 2.0 release aimed at inferring longitudinal clonal trees enhances the original framework with new key functionalities: an improved data management for preprocessing of standard variant calling data, a reworked inference engine, and direct connection to public databases. Conclusions All of this is accessible through a new and interactive Shiny R graphical interface offering the possibility to apply filters helpful in discriminating relevant or potential driver mutations, set up inferential parameters, and visualize the results. The software is available at: github.com/BIMIB-DISCo/LACE .

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Algorithms / Bioinformatics / Biomedical and Life Sciences / Cancer / Clonal analysis / Clone Cells / Cloning / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer applications / Data management / Evolution / Experiments / Genomes / Humans / Inference / Interface / Life Sciences / Longitudinal / Longitudinal studies / Metadata / Microarrays / Mutation / Neoplasms - genetics / Shiny / Single cell / Software