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Comparative Lesions Analysis Through a Targeted Sequencing Approach

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

Clonality inference in multiple tumor samples using phylogeny.

Salem Malikic¹, Andrew W McPherson¹, Nilgun Donmez¹

¹School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, BC Cancer Agency, Vancouver, BC, Canada, Vancouver Prostate Center, Vancouver, BC, Canada and School of Informatics and Computing, Indiana University, Bloomington, IN, USA.

Bioinformatics (Oxford, England)

|January 9, 2015

Summary

This summary is machine-generated.

Determining cancer’s internal genetic diversity (intra-tumor heterogeneity) is hard. A new computational method, CITUP, accurately identifies cancer cell populations and their evolutionary relationships using phylogenetic constraints.

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Area of Science:

Computational biology
Cancer genomics
Evolutionary biology

Background:

Intra-tumor heterogeneity arises from evolving subclones during cancer progression.
Understanding this heterogeneity is crucial for clinical applications.
Accurate computational determination of clonal subpopulations remains a significant challenge.

Purpose of the Study:

To develop a novel computational method for inferring clonal populations and their frequencies within tumors.
To address the challenge of determining intra-tumor heterogeneity using in silico approaches.
To satisfy phylogenetic constraints and leverage multi-sample data for improved accuracy.

Main Methods:

A combinatorial method named clonality inference in tumors using phylogeny (CITUP) was developed.
CITUP infers clonal populations and their frequencies.
The method incorporates phylogenetic constraints and utilizes data from multiple samples.

Main Results:

CITUP was validated using simulated datasets.
The method demonstrated high accuracy in predicting clonal frequencies and underlying phylogeny on real deep sequencing data from two cancer studies.
CITUP successfully infers clonal populations and their frequencies.

Conclusions:

CITUP is a novel and accurate computational tool for analyzing intra-tumor heterogeneity.
The method effectively infers clonal populations and their evolutionary history.
CITUP has the potential to advance cancer research and clinical applications by providing insights into tumor evolution.