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A Practical Guide to Phylogenetics for Nonexperts
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Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees
Camir Ricketts1,2, Victoria Popic3, Hosein Toosi4
1Tri-I Computational Biology & Medicine Graduate Program, Cornell University, New York, New York.
Current Protocols in Bioinformatics
|June 22, 2018
Summary
Reconstructing cancer evolution and phylogeny is complex. Two new tools, LICHeE and BAMSE, use variant allele fractions from somatic mutations to infer cancer phylogenies, with installation and usage guidelines provided.
Area of Science:
- Computational biology
- Cancer genomics
- Evolutionary medicine
Background:
- Cancer evolution is characterized by genetic alterations and clonal heterogeneity.
- Accurate reconstruction of cancer phylogeny is crucial for understanding disease progression and developing targeted therapies.
- Existing computational methods face challenges in inferring complex evolutionary trajectories.
Purpose of the Study:
- To provide comprehensive guidelines for installing and utilizing two novel computational tools, LICHeE and BAMSE.
- To facilitate the reconstruction of cancer phylogeny trees and the quantification of cancer evolution.
- To enable researchers to effectively apply these tools for analyzing somatic mutations across multiple samples.
Main Methods:
- LICHeE and BAMSE utilize estimated variant allele fraction (VAF) of somatic mutations.
- These tools infer the most likely cancer phylogenies by analyzing VAF data across multiple samples.
- The study focuses on providing practical instructions for tool installation and execution.
Main Results:
- Guidelines for installing and running LICHeE and BAMSE are presented.
- The tools enable the inference of cancer phylogenies based on VAF data.
- Successful application of these tools aids in quantifying cancer evolution.
Conclusions:
- LICHeE and BAMSE offer valuable computational approaches for cancer phylogeny reconstruction.
- These tools assist in understanding the evolutionary dynamics of cancer.
- The provided guidelines ensure accessibility and usability for researchers in the field.
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