Sensitivity to sequencing depth in single-cell cancer genomics

Abstract

BackgroundQuerying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the quality of single-cell data are critically needed. Taking advantage of five published single-cell whole-genome and whole-exome cancer datasets, we studied the impact of sequencing depth and sampling effort towards single-cell variant detection, including structural and driver mutations, genotyping accuracy, clonal inference and phylogenetic reconstruction, using recent tools specifically designed for single-cell data.\n\nResultsAltogether, our results suggest that, for relatively large sample sizes (25 or more cells), sequencing single tumor cells at depths >5x does not drastically improve somatic variant discovery, the characterization of clonal genotypes or the estimation of phylogenies from single tumor cells.\n\nConclusionsWe demonstrate that sequencing many individual tumor cells at a modest depth represents an effective alternative to explore the mutational landscape and clonal evolutionary patterns of cancer genomes, without the excessively high costs associated with high-coverage genome sequencing.