Inferring copy number variation from gene expression data: methods, comparisons, and applications to oncology
Joseph, Boen, Wagner, Joel and Di Nanni, Noemi (2021) Inferring copy number variation from gene expression data: methods, comparisons, and applications to oncology. bioRxiv.
Abstract
Copy number variations (CNVs) are genomic events where the number of copies of a particular gene varies from cell to cell. Cancer cells are associated with somatic CNV changes resulting in gene amplifications and gene deletions. However, short of single-cell whole-genome sequencing, it is difficult to detect and quantify CNV events in single cells. In contrast, the rapid development of single-cell RNA sequencing (scRNA-seq) technologies has enabled easy acquisition of single-cell gene expression data. In this work, we employ three methods to infer CNV events from scRNA-seq data and provide a statistical comparison of the methods’ results. In addition, we combine the analysis of scRNA-seq and inferred CNV data to visualize and determine subpopulations and heterogeneity in tumor cell populations.
Item Type: | Article |
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Keywords: | single-cell RNA-seq, scRNA-seq, oncology, copy number variation, CNV |
Date Deposited: | 02 Mar 2022 00:45 |
Last Modified: | 02 Mar 2022 00:45 |
URI: | https://oak.novartis.com/id/eprint/46003 |