SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing.

ABSTRACT: 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 o

SUBMITTER: Wang R 

PROVIDER: S-EPMC7250054 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature