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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..ORCID iD: 0000-0003-4575-5629
Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
Uppsala Univ, Dept Cell & Mol Biol, Natl Bioinformat Infrastruct Sweden, Scilifelab, Uppsala, Sweden..
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2019 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 20, article id 68Article in journal (Refereed) Published
Abstract [en]

Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Comparing the performance of Conbase to three other methods, we find that Conbase performs best in terms of false discovery rate and specificity and provides superior robustness on simulated data, in vitro expanded fibroblasts and clonal lymphocyte populations isolated directly from a healthy human donor.

Place, publisher, year, edition, pages
BMC , 2019. Vol. 20, article id 68
Keywords [en]
Single-cell DNA sequencing, Single-cell variant calling, Somatic variation
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:kth:diva-249805DOI: 10.1186/s13059-019-1673-8ISI: 000463101600001PubMedID: 30935387Scopus ID: 2-s2.0-85063796386OAI: oai:DiVA.org:kth-249805DiVA, id: diva2:1306505
Note

QC 20190424

Available from: 2019-04-24 Created: 2019-04-24 Last updated: 2019-04-24Bibliographically approved

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Borgström, Erik

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