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SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing.
Wang, Rujin; Lin, Dan-Yu; Jiang, Yuchao.
Afiliación
  • Wang R; Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
  • Lin DY; Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
  • Jiang Y; Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address: yuchaoj@email.unc.edu.
Cell Syst ; 10(5): 445-452.e6, 2020 05 20.
Article en En | MEDLINE | ID: mdl-32437686
Whole-genome single-cell DNA sequencing (scDNA-seq) enables characterization of copy-number profiles at the cellular level. We propose SCOPE, a normalization and copy-number estimation method for the noisy scDNA-seq data. SCOPE's main features include the following: (1) a Poisson latent factor model for normalization, which borrows information across cells and regions to estimate bias, using in silico identified negative control cells; (2) an expectation-maximization algorithm embedded in the normalization step, which accounts for the aberrant copy-number changes and allows direct ploidy estimation without the need for post hoc adjustment; and (3) a cross-sample segmentation procedure to identify breakpoints that are shared across cells with the same genetic background. We evaluate SCOPE on a diverse set of scDNA-seq data in cancer genomics and show that SCOPE offers accurate copy-number estimates and successfully reconstructs subclonal structure. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Análisis de Secuencia de ADN / Variaciones en el Número de Copia de ADN / Análisis de la Célula Individual Límite: Humans Idioma: En Revista: Cell Syst Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Análisis de Secuencia de ADN / Variaciones en el Número de Copia de ADN / Análisis de la Célula Individual Límite: Humans Idioma: En Revista: Cell Syst Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos