Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

Davis J. McCarthy, Raghd Rostom, Yuanhua Huang, Daniel J. Kunz, Petr Danecek, Marc Jan Bonder, Tzachi Hagai, Ruqian Lyu, , Wenyi Wang, Daniel J. Gaffney, Benjamin D. Simons, Oliver Stegle (Lead / Corresponding author), Sarah A. Teichmann (Lead / Corresponding author)

Research output: Contribution to journalArticle

Abstract

Bulk and single-cell DNA sequencing has enabled reconstructing clonal substructures of somatic tissues from frequency and cooccurrence patterns of somatic variants. However, approaches to characterize phenotypic variations between clones are not established. Here we present cardelino (https://github.com/single-cell-genetics/cardelino), a computational method for inferring the clonal tree configuration and the clone of origin of individual cells assayed using single-cell RNA-seq (scRNA-seq). Cardelino flexibly integrates information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. We apply cardelino to a published cancer dataset and to newly generated matched scRNA-seq and exome-seq data from 32 human dermal fibroblast lines, identifying hundreds of differentially expressed genes between cells from different somatic clones. These genes are frequently enriched for cell cycle and proliferation pathways, indicating a role for cell division genes in somatic evolution in healthy skin.

Original languageEnglish
Pages (from-to)414-421
Number of pages8
JournalNature Methods
Volume17
Issue number4
DOIs
Publication statusPublished - 16 Mar 2020

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    McCarthy, D. J., Rostom, R., Huang, Y., Kunz, D. J., Danecek, P., Bonder, M. J., Hagai, T., Lyu, R., Wang, W., Gaffney, D. J., Simons, B. D., & Stegle, O., & Teichmann, S. A. (2020). Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes. Nature Methods, 17(4), 414-421. https://doi.org/10.1038/s41592-020-0766-3