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Ramakrishnan, A. ; Symeonidi, A. ; Hanel, P. ; Schmid, K.T.* ; Richter, M.L.* ; Schubert, M.* ; Colomé-Tatché, M.

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

Nat. Commun. 14:5846 (2023)
Publ. Version/Full Text DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Aneuploidy Paradox; Chromatin
ISSN (print) / ISBN 2041-1723
e-ISSN 2041-1723
Journal Nature Communications
Quellenangaben Volume: 14, Issue: 1, Pages: , Article Number: 5846 Supplement: ,
Publisher Nature Publishing Group
Publishing Place London
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Grants Helmholtz Association
Impuls-und Vernetzungsfonds of the Helmholtz-Gemeinschaft
We would like to thank Dr. Antonio Scialdone for discussions about calling CNAs in scRNA-seq data, and Anna Danese for help in embedding of scATAC-seq data. We thank Dr. Andres Castellanos for the discussions regarding the BCC tumor composition. We thank