scPlOver: inferring DNA content from amplification-free single-cell WGS using fragment overlaps

Correctly inferring copy-number aberrations from single-cell DNA sequencing data requires estimating cellular DNA content, which is unidentifiable from read counts alone. In tagmentation-based sequencing, each fragment represents a distinct DNA molecule, thus fragment overlaps provide an orthogonal signal for copy number. We present a theoretical model of fragment overlaps as a function of copy number and coverage and introduce scPlOver, a method that uses this model to infer DNA content. scPlOver outperforms existing approaches on simulated and experimental datasets and identifies thousands of ovarian cancer cells with higher DNA content than previously estimated across a cohort of 41 patients.