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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing

By Joanna Hård, Ezeddin Al Håkim, Marie Kindblom, Åsa K. Björklund, Ilke Demirci, Marta Paterlini, Pedro Reu, Bengt Sennblad, Erik Borgström, Patrik L Ståhl, Jakob Michaelsson, Jeff E. Mold, Jonas Frisén

Posted 05 Feb 2018
bioRxiv DOI: 10.1101/259994 (published DOI: 10.1186/s13059-019-1673-8)

Here we report the development of Conbase, a software application for the identification of somatic mutations in single cell DNA sequencing data with high rates of allelic dropout and at low read depth. Conbase leverages data from multiple samples in a dataset and utilizes read phasing to call somatic single nucleotide variants and to accurately predict genotypes in whole genome amplified single cells in somatic variant loci. We demonstrate the accuracy of Conbase on simulated datasets, in vitro expanded fibroblasts and clonally in vivo expanded lymphocyte populations isolated directly from a healthy human donor.

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