PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors.

ABSTRACT: The combination of bulk and single-cell DNA sequencing data of the same tumor enables the inference of high-fidelity phylogenies that form the input to many important downstream analyses in cancer genomics. While many studies simultaneously perform bulk and single-cell sequencing, some studies have analyzed initial bulk data to identify which mutations to target in a follow-up single-cell sequencing experiment, thereby decreasing cost. Bulk data provide an additional untapped source of valuable information, composed of candidate phylogenies and associated clonal prevalence. Here, we introduce PhyDOSE, a method that uses this information to strategically optimize the design of follow-up single cell experiments. Underpinning our method is the observation that only a small number of clones un

SUBMITTER: Weber LL 

PROVIDER: S-EPMC7553321 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature