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

Genome Biology

Jakob Michaelsson¹  Ezeddin Al Hakim²  Marta Paterlini²  Jonas Frisén²  Patrik L. Ståhl²  Pedro Reu²  Joanna Hård²  Marie Kindblom²  Ilke Demirci²  Jeff E. Mold²  Bengt Sennblad³  Åsa K. Björklund³  Erik Borgström⁴ 

[1] Center for Infectious Medicine, Department of Medicine, Karolinska Institutet;Department of Cell and Molecular Biology, Karolinska Institutet;Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Scilifelab, Uppsala University;Division of Gene Technology, Scilifelab, KTH Royal Institute of Technology;

关键词: Single-cell DNA sequencing;    Single-cell variant calling;    Somatic variation;   

DOI  :  10.1186/s13059-019-1673-8

来源: DOAJ

【 摘 要 】

Abstract 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.

【 授权许可】

Unknown