CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications
Abstract
Somatic copy number alterations (CNAs) are a hallmark of cancer, but their role in tumorigenesis and clinical relevance remain largely unclear. Here, we developed CNApp, a web-based tool that allows a comprehensive exploration of CNAs by using purity-corrected segmented data from multiple genomic platforms. CNApp generates genome-wide profiles, computes CNA scores for broad, focal and global CNA burdens, and uses machine learning-based predictions to classify samples. We applied CNApp to the TCGA pan-cancer dataset of 10,635 genomes showing that CNAs classify cancer types according to their tissue-of-origin, and that each cancer type shows specific ranges of broad and focal CNA scores. Moreover, CNApp reproduces recurrent CNAs in hepatocellular carcinoma and predicts colon cancer molecular subtypes and microsatellite instability based on broad CNA scores and discrete genomic imbalances. In summary, CNApp facilitates CNA-driven research by providing a unique framework to identify relevant clinical implications. CNApp is hosted at https://tools.idibaps.org/CNApp/.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jan 15, 2020
- Source ID
- 10.7554/elife.50267
Entities
People
- Antoni Castells
- Eva Hernández-illán
- Jordi Camps
- Josep Maria Llovet
- Juan José Lozano
- Laia Bassaganyas
- Marcos Díaz-Gay
- Maria Vila-casadesús
- Roger Esteban-fabró
- Sebastià Franch-Expósito
- Sergi Castellví-bel
Organizations
- Autonomous University of Barcelona
- Catalan Institution for Research and Advanced Studies
- Centro de Investigación Biomédica en Red
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas
- European Commission
- European Regional Development Fund
- Framework Programmes for Research and Technological Development
- Generalitat of Catalonia
- National Cancer Institute
- Samuel Waxman Cancer Research Foundation
- Spanish Association Against Cancer
- United States Department of Defense
- University of Barcelona