Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

Single-cell multiple displacement amplification (SCMDA) and a tool for single-nucleotide-variant calling (SCcaller) dramatically decrease artifacts in genome-wide variant calling from single cells. Mutation analysis in single-cell genomes is prone to artifacts associated with cell lysis and whole-genome amplification. Here we addressed these issues by developing single-cell multiple displacement amplification (SCMDA) and a general-purpose single-cell-variant caller, SCcaller ( https://github.com/biosinodx/SCcaller/ ). By comparing SCMDA-amplified single cells with unamplified clones from the same population, we validated the procedure as a firm foundation for standardized somatic-mutation analysis in single-cell genomics.