Copy-scAT: Deconvoluting single-cell chromatin accessibility of genetic subclones in cancer.

ABSTRACT: Single-cell epigenomic assays have tremendous potential to illuminate mechanisms of transcriptional control in functionally diverse cancer cell populations. However, application of these techniques to clinical tumor specimens has been hampered by the current inability to distinguish malignant from nonmalignant cells, which potently confounds data analysis and interpretation. Here, we describe Copy-scAT, an R package that uses single-cell epigenomic data to infer copy number variants (CNVs) that define cancer cells. Copy-scAT enables studies of subclonal chromatin dynamics in complex tumors like glioblastoma. By deploying Copy-scAT, we uncovered potent influences of genetics on chromatin accessibility profiles in individual subclones. Consequently, some genetic subclones were predisposed to

SUBMITTER: Nikolic A 

PROVIDER: S-EPMC8514091 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature