RT Journal Article
SR Electronic
T1 Copy-scAT: An R package for detection of large-scale and focal copy number alterations in single-cell chromatin accessibility datasets
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.21.305516
DO 10.1101/2020.09.21.305516
A1 Ana Nikolic
A1 Divya Singhal
A1 Katrina Ellestad
A1 Michael Johnston
A1 Aaron Gillmor
A1 Sorana Morrissy
A1 Jennifer A Chan
A1 Paola Neri
A1 Nizar Bahlis
A1 Marco Gallo
YR 2020
UL http://biorxiv.org/content/early/2020/09/22/2020.09.21.305516.abstract
AB The single-cell assay for transposase accessible chromatin (scATAC) is an invaluable asset to profile the epigenomic landscape of heterogeneous cells populations in complex tissue and organ systems. However, the lack of tools that enable the use of scATAC data to discriminate between malignant and non-malignant cells has prevented the widespread application of this technique to clinical tumor samples. Here we describe Copy-scAT, a new computational tool that uses scATAC data to infer both large-scale and focal copy number alterations. Copy-scAT can call both clonal and subclonal copy number changes, allowing identification of cancer cells and cell populations that putatively constitute the tumor microenvironment. Copy-scAT therefore enables downstream chromatin accessibility studies that focus on malignant or non-malignant cell populations in clinical samples that are profiled by scATAC.Competing Interest StatementThe authors have declared no competing interest.