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Related Experiment Video

Updated: Feb 23, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Tumor phylogeny inference using tree-constrained importance sampling.

Gryte Satas¹, Benjamin J Raphael²

¹Department of Computer Science, Brown University, Providence, RI, USA.

Bioinformatics (Oxford, England)

|September 9, 2017

Summary

This summary is machine-generated.

We developed a new algorithm, PASTRI, to reconstruct tumor evolution from bulk sequencing data. It accurately infers phylogenetic trees, outperforming existing methods and offering insights into cancer development.

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Last Updated: Feb 23, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

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Published on: October 16, 2018

Area of Science:

Evolutionary Biology
Genomics
Computational Biology

Background:

Tumorigenesis is an evolutionary process.
Reconstructing tumor phylogeny is difficult due to cellular heterogeneity in bulk sequencing data.

Purpose of the Study:

To introduce a novel algorithm, Probabilistic Algorithm for Somatic Tree Inference (PASTRI), for inferring tumor phylogenetic trees from bulk sequencing data.
To cluster somatic mutations into distinct clones and reconstruct tumor evolutionary history.

Main Methods:

PASTRI employs an importance sampling algorithm.
It integrates a probabilistic model of DNA sequencing data with an enumeration algorithm based on phylogenetic tree constraints.

Main Results:

PASTRI achieves fast, accurate, and noise-robust phylogenetic tree inference.
It outperforms existing cancer phylogeny algorithms in runtime and accuracy on simulated data.
On real chronic lymphocytic leukemia (CLL) data, PASTRI supported a linear phylogeny over a previously proposed complex branching one.

Conclusions:

PASTRI offers a robust method for phylogenetic tree inference from mixed tumor samples.
The algorithm provides a powerful tool for understanding tumor evolution.