PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation

bioRxiv (Cold Spring Harbor Laboratory) 2026 Preprint Open access

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Authors: Pablo Bousquets-Muñoz, Heather E. Grant, Darryl Shibata, Trevor A Graham, Carlo C. Maley, Calum Gabbutt, Diego Mallo
DOI: 10.64898/2026.05.05.722981
Cited by: 1
References: 18

Abstract

We present PHYFUM, a novel Bayesian phylogenetic method for methylation data that reconstructs the evolutionary history of stem cells and the glandular structures they reside within in normal tissue. Using simulations, we validated this phylogenetic method and confirmed its accuracy. A re-analysis of 22 patients unveiled early gland divergence in the human gut, in contrast to a much later common ancestor in the endometrium, and yielded strong evidence against gland division by segregation of individual stem cells.

Fields of Study & Subjects

Epigenetics and DNA Methylation Genetic factors in colorectal cancer Cancer Genomics and Diagnostics

Publication details

Journal / source
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Publication date
7 May 2026
Language
EN
Document type
Preprint