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| Home > Articles > Published articles > CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications |
(Institut d'Investigacions Biomèdiques August Pi i Sunyer) (Institut d'Investigacions Biomèdiques August Pi i Sunyer) (Institut d'Investigacions Biomèdiques August Pi i Sunyer) (Institut d'Investigacions Biomèdiques August Pi i Sunyer) (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia)
| Date: | 2020 |
| 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 . In most cases, human cells contain two copies of each of their genes, yet sometimes this can change, an effect called copy number alteration (CNA). Cancer is a genetic disease and thus, studying the DNA from tumor samples is crucial to improving diagnosis and choosing the right treatment. Most tumors contain cells with CNAs; however, the impact of CNAs in cancer progression is poorly understood. CNAs can be studied by examining the genome of tumor cells and finding which regions display an unusual number of copies. It may also be possible to gather information about different cancer types by analyzing the CNAs in a tumor, but this approach requires the analysis of large amounts of data. To aid the analysis of CNAs in cancer cells, Franch-Expósito, Bassaganyas et al. have created an online tool called CNApp, which is able to identify and count CNAs in genomic data and link them to features associated with different cancers. The hope is that a better understanding of the effect of CNAs in cancer could help better diagnose cancers, and improve outcomes for patients. Potentially, this could also predict what type of treatment would work better for a specific tumor. Besides, by using a machine-learning approach, the tool can also make predictions about specific cancer subtypes in order to facilitate clinical decisions. Franch-Expósito, Bassaganyas et al. tested CNApp using previously existing cancer data from 33 different cancer types to show how CNApp can help the interpretation of CNAs in cancer. Moreover, CNApp can also use CNAs to identify different types of bowel (colorectal) cancer in a way that could help doctors to make decisions about treatment. Together these findings show that CNApp provides an adaptable and accessible research tool for the study of cancer genomics, which could provide opportunities to inform medical procedures. |
| Grants: | Agència de Gestió d'Ajuts Universitaris i de Recerca 2016BP00161 Agència de Gestió d'Ajuts Universitaris i de Recerca 2018FI-B1_00213 European Commission PCIG11-GA-2012-321937 Ministerio de Economía y Competitividad FPI-BES-2017-081286 Instituto de Salud Carlos III CP13/00160 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017SGR1035 Agència de Gestió d'Ajuts Universitaris i de Recerca SLT002/16/00398 European Commission HEPCAR/667273-2 Ministerio de Economía y Competitividad SAF2016-76390 Agència de Gestió d'Ajuts Universitaris i de Recerca SGR-1162 Agència de Gestió d'Ajuts Universitaris i de Recerca SGR-1358 Instituto de Salud Carlos III PI14/00783 Instituto de Salud Carlos III PI17/01304 Instituto de Salud Carlos III PI17/00878 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017SGR21 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017SGR653 |
| Rights: | Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.  |
| Language: | Anglès |
| Document: | Article ; recerca ; Versió publicada |
| Subject: | Copy number alterations ; Cancer genomics ; CNA scores ; Pan-cancer ; Colorectal cancer ; Hepatocellular carcinoma ; Human |
| Published in: | eLife, Vol. 9 (january 2020) , ISSN 2050-084X |
