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) 2016
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Abstract

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 (https://bitbucket.org/aroth85/scg), 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.