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Nat Methods. 2016 Jul;13(7):573-6. doi: 10.1038/nmeth.3867. Epub 2016 May 16.

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

Author information

1
Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.
2
Graduate Bioinformatics Training Program, University of British Columbia, Vancouver, British Columbia, Canada.
3
School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.
4
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
5
Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, British Columbia, Canada.
6
Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada.
7
Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.

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.

PMID:
27183439
DOI:
10.1038/nmeth.3867
[Indexed for MEDLINE]

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