CiberAMP: An R Package to Identify Differential mRNA Expression Linked to Somatic Copy Number Variations in Cancer Datasets

• Published in: Biology (Basel, Switzerland) Vol. 11; no. 10; p. 1411
• Main Authors: Caloto, Rubén, Lorenzo-Martín, L. Francisco, Quesada, Víctor, Carracedo, Arkaitz, Bustelo, Xosé R.
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 28.09.2022; MDPI
• Subjects: Algorithms; Bioinformatics; Cancer; Copy number; Datasets; Gene expression; Genetic diversity; Genomes; Genomics; Glioblastoma; Maximum likelihood method; pan-cancer; RNA sequencing; software; transcriptome; Transcriptomics; Tumors
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology11101411

Somatic copy number variations (SCNVs) are genetic alterations frequently found in cancer cells. These genetic alterations can lead to concomitant perturbations in the expression of the genes included in them and, as a result, promote a selective advantage to cancer cells. However, this is not always the case. Due to this, it is important to develop in silico tools to facilitate the accurate identification and functional cataloging of gene expression changes associated with SCNVs from pan-cancer data. Here, we present a new R-coded tool, designated as CiberAMP, which utilizes genomic and transcriptomic data contained in the Cancer Genome Atlas (TCGA) to identify such events. It also includes information on the genomic context in which such SCNVs take place. By doing so, CiberAMP provides clues about the potential functional relevance of each of the SCNV-associated gene expression changes found in the interrogated tumor samples. The main features and advantages of this new algorithm are illustrated using glioblastoma data from the TCGA database.