epiAneufinder identifies copy number alterations from single-cell ATAC-seq data

Akshaya Ramakrishnan, Aikaterini Symeonidi (), Patrick Hanel, Katharina T. Schmid, Maria L. Richter, Michael Schubert and Maria Colomé-Tatché ()
Additional contact information
Akshaya Ramakrishnan: Helmholtz Zentrum München, German Research Center for Environmental Health
Aikaterini Symeonidi: Helmholtz Zentrum München, German Research Center for Environmental Health
Patrick Hanel: Helmholtz Zentrum München, German Research Center for Environmental Health
Katharina T. Schmid: Faculty of Medicine, LMU Munich
Maria L. Richter: Faculty of Medicine, LMU Munich
Michael Schubert: Netherlands Cancer Institute
Maria Colomé-Tatché: Helmholtz Zentrum München, German Research Center for Environmental Health

Nature Communications, 2023, vol. 14, issue 1, 1-10

Abstract: Abstract Single-cell open chromatin profiling via scATAC-seq has become a mainstream measurement of open chromatin in single-cells. Here we present epiAneufinder, an algorithm that exploits the read count information from scATAC-seq data to extract genome-wide copy number alterations (CNAs) for individual cells, allowing the study of CNA heterogeneity present in a sample at the single-cell level. Using different cancer scATAC-seq datasets, we show that epiAneufinder can identify intratumor clonal heterogeneity in populations of single cells based on their CNA profiles. We demonstrate that these profiles are concordant with the ones inferred from single-cell whole genome sequencing data for the same samples. EpiAneufinder allows the inference of single-cell CNA information from scATAC-seq data, without the need of additional experiments, unlocking a layer of genomic variation which is otherwise unexplored.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-023-41076-1 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41076-1

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-023-41076-1

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().