Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers.

ABSTRACT: Epithelial cancers are typically heterogeneous with primary prostate cancer being a typical example of histological and genomic variation. Prior studies of primary prostate cancer tumour genetics revealed extensive inter and intra-patient genomic tumour heterogeneity. Recent advances in machine learning have enabled the inference of ground-truth genomic single-nucleotide and copy number variant status from transcript data. While these inferred SNV and CNV states can be used to resolve clonal phylogenies, however, it is still unknown how faithfully transcript-based tumour phylogenies reconstruct ground truth DNA-based tumour phylogenies. We sought to study the accuracy of inferred-transcript to recapitulate DNA-based tumour phylogenies. We first performed in-silico comparisons of inferred a

SUBMITTER: Erickson A 

PROVIDER: S-EPMC11698422 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature