Marker selection strategies for circulating tumor DNA guided by phylogenetic inference.

ABSTRACT:

Motivation

Blood-based profiling of tumor DNA ("liquid biopsy") offers great prospects for non-invasive early cancer diagnosis and clinical guidance, but requires further computational advances to become a robust quantitative assay of tumor clonal evolution. We propose new methods to better characterize tumor clonal dynamics from circulating tumor DNA (ctDNA), through application to two specific tasks: (i) applying longitudinal ctDNA data to refine phylogeny models of clonal evolution, and (ii) quantifying changes in clonal frequencies that may be indicative of treatment response or tumor progression. We pose these through a probabilistic framework for optimally identifying markers and using them to characterize clonal evolution.

Results

We first estimate a density over clon

SUBMITTER: Fu X 

PROVIDER: S-EPMC12002908 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature