title: Clonal genotype and population structure inference from single-cell tumor sequencing.
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.
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|Graduate Bioinformatics Training Program, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Andrew
authors.initials: A
authors.lastname: Roth
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Andrew
authors.identifier: 0000-0002-5654-5101
authors.initials: A
authors.lastname: McPherson
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Emma
authors.initials: E
authors.lastname: Laks
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Justina
authors.initials: J
authors.lastname: Biele
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Damian
authors.identifier: 0000-0002-5370-4592
authors.initials: D
authors.lastname: Yap
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Adrian
authors.initials: A
authors.lastname: Wan
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Maia A
authors.initials: MA
authors.lastname: Smith
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Cydney B
authors.initials: CB
authors.lastname: Nielsen
authors.affiliation: Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Jessica N
authors.initials: JN
authors.lastname: McAlpine
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Samuel
authors.initials: S
authors.lastname: Aparicio
authors.affiliation: Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Bouchard-Côté
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.|Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Sohrab P
authors.identifier: 0000-0001-6402-523X
authors.initials: SP
authors.lastname: Shah
mesh_terms: D002999:Clone Cells; D018284:Cystadenocarcinoma, Serous / Q000235:genetics*; D005260:Female; D015894:Genome, Human; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D007938:Leukemia / Q000235:genetics*; D042361:Mammary Glands, Human / Q000378:metabolism*; D015233:Models, Statistical; D010051:Ovarian Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software