Clonal genotype and population structure inference from single-cell tumor sequencing.

Andrew Roth, Andrew McPherson, Emma Laks, Justina Biele, Damian Yap, Adrian Wan, Maia A Smith, Cydney B Nielsen, Jessica N McAlpine, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P Shah, Nature methods 13, 573-6 (2016)


Single-cell DNA sequencing has great potential to reveal the clonal genotypes and population structure of human cancers. However, single-cell data suffer from missing values and biased allelic counts as well as false genotype measurements owing to the sequencing of multiple cells. We describe the Single Cell Genotyper (, an open-source software based on a statistical model coupled with a mean-field variational inference method, which can be used to address these problems and robustly infer clonal genotypes.