Journal article

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

Davis McCarthy, Raghd Rostom, Yuanhua Huang, Daniel Kunz, Petr Danecek, Marc Jan Bonder, Tzachi Hagai, Wenyi Wang, Daniel Gaffney, Benjamin Simons, Oliver Stegle, Sarah Teichmann, undefined HipSci Consortium

Published : 2018

Abstract

Decoding the clonal substructures of somatic tissues sheds light on cell growth, development and differentiation in health, ageing and disease. DNA-sequencing, either using bulk or using single-cell assays, has enabled the reconstruction of clonal trees from frequency and co-occurrence patterns of somatic variants. However, approaches to systematically characterize phenotypic and functional variations between individual clones are not established. Here we present cardelino ( https://github.com/PMBio/cardelino ), a computational method for inferring the clone of origin of individual cells that have been assayed using single-cell RNA-seq (scRNA-seq). After validating our model using simulation..

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University of Melbourne Researchers

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