Phylogenetic tree reconstruction

Overview

Computational method applied to multiregion tumor sequencing data to infer the evolutionary history of tumor cell populations. Mutation presence/absence calls across regions are used to build phylogenetic trees (e.g., by maximum parsimony), distinguishing truncal (shared by all regions) from branch (subclonal) alterations.

Used by

Maximum parsimony phylogenetic trees built from regional mutation presence/absence calls across 10 ccRCC tumors (79 samples); used to classify driver mutations and SCNAs as truncal vs. branch and to identify parallel evolution events (e.g., independent PIK3CA hotspot mutations in EV005, convergent SETD2 hits in 3 tumors) PMID:24487277.
MrBayes 3.2 used for single-cell Bayesian phylogenetic inference on SA494 and SA501 breast cancer PDX nuclei; confirmed pre-existing minor tumor clones as the origin of xenograft-dominant populations and resolved 5 clonal genotypes across serial passages of SA501 PMID:25470049
Multi-region phylogenetic analysis of WGS data from 2 gastric cancer patients (3 primary-tumor regions + 2 lymph-node metastases each) showed substantial divergence among primary regions with lymph-node metastases sharing a common clonal ancestor from only one primary-tumor region PMID:25583476
Phylogenetic trees constructed with CITUP (v0.1.0) plus manual reconstruction in TRACERx to resolve monoclonal vs polyclonal relapse seeding patterns detectable from post-operative plasma ctDNA PMID:28445469

Notes

Maximum parsimony is appropriate for tumor phylogenetics when SNP-array integer copy-number resolution is limited.
Parallel (convergent) driver hits across independent branches can be misinterpreted as single truncal events without multiregion data PMID:24487277.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:25470049

This page was processed by crosslinker on 2026-05-14. - PMID:25583476

This page was processed by crosslinker on 2026-05-14. - PMID:28445469

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