Deconvolution and phylogeny inference of diverse variant types integrating bulk DNA-seq with single-cell RNA-seq.

ABSTRACT:

Motivation

Reconstructing clonal lineage trees ("tumor phylogenetics") has become a core tool of cancer genomics. Earlier approaches based on bulk DNA sequencing (DNA-seq) have largely given way to single-cell DNA-seq (scDNA-seq), which offers far greater resolution for clonal substructure. Available data has lagged behind computational theory, though. While single-cell RNA-seq (scRNA-seq) has become widely available, scDNA-seq remains costly and technically challenging, precluding routine use on large cohorts. This forces tradeoffs between the limited genome coverage of scRNA-seq, limited availability of scDNA-seq, and limited clonal resolution of bulk DNA-seq. These limitations are especially problematic for studying structural variations and focal copy number variations that are

SUBMITTER: Bristy NA 

PROVIDER: S-EPMC12571511 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature