DOI: 10.1101/479667Nov 27, 2018Paper

CNApp: quantification of genomic copy number alterations in cancer and integrative analysis to unravel clinical implications

BioRxiv : the Preprint Server for Biology
Sebastia Franch-ExpositoJordi Camps

Abstract

Somatic copy number alterations (CNAs) are a hallmark of cancer. Although CNA profiles have been established for most human tumor types, their precise role in tumorigenesis as well as their clinical and therapeutic relevance remain largely unclear. Thus, computational and statistical approaches are required to thoroughly define the interplay between CNAs and tumor phenotypes. Here we developed CNApp, a user-friendly web tool that offers sample- and cohort-level computational analyses, allowing a comprehensive and integrative exploration of CNAs with clinical and molecular variables. 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 a pan-cancer dataset of 10,635 genomes from TCGA showing that CNA patterns classify cancer types according to their tissue-of-origin, and that broad and focal CNA scores positively correlate in samples with low amounts of whole-chromosome and chromosomal arm-level imbalances. Moreover, using the hepatocellular carcinoma cohort from the TCGA repository, we demonstrate the reliability of the tool i...Continue Reading

Related Concepts

DNA, Complementary
Malignant Neoplasms
Chromosomes
Genome
Neoplasms
Research
Software Tools
deoxy(thymidylyl-cytidylyl-guanylyl-adenylic acid)
beta-chlornaltrexamine
Autonomic Nervous System Imbalance

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