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 Nikolic, Ana
A1 Singhal, Divya
A1 Ellestad, Katrina
A1 Johnston, Michael
A1 Gillmor, Aaron
A1 Morrissy, Sorana
A1 Chan, Jennifer A
A1 Neri, Paola
A1 Bahlis, Nizar
A1 Gallo, Marco
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.