Cancer phylogenetics: Computational modeling of tumor evolution
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2012
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Nova Science Publishers, Inc.
Abstract
The field of phylogenetics is one of the core areas of Bioinformatics which deals with computational methods to infer evolutionary heritage of organisms and genes. While phylogenetics has been extensively utilized in taxonomy and systematics of organisms, it is only very recently that the system started expanding to other fields- most importantly in cancer biology where it profoundly transformed our understanding of clonal evolution. Many of our findings in cancer phylogenetics credit to the fact that the tumor is not merely a collection of transformed cells with random mutation events; rather it is an evolving population. Many of the facets underpinning modern evolutionary synthesis can be applied to classify cancers and track its progression from initiating somatic mutation to symptomatic neoplasm. It is now widely accepted that all sub-clones within cancer are phylogenetically related and probability of a particular sub-clone progressing into neoplasm depending upon its time of initiation and evolutionary fitness. Computational models of tumor evolution have also contributed in identifying common clades- "cancer sub-types"- associated with particular cancers in different patients that in turn helped in translating our understanding of oncogeny to the development of "targeted therapeutics"- rationally designed drugs that are molecularly targeted to particular sub-types. Advent of next generation ultra-deep genome sequencing technologies has been rapidly trans-forming the very landscape of cancer phyogenetics. This chapter introduces the concept of cancer phylogenetics and reviews some of the recent advances in this field. This chapter also summarizes various phylogenetic approaches including distance matrix methods, parsimony, maximum likelihood, Bayesian methods and probabilistic inference that have potential applications in cancer research. ? 2012 Nova Science Publishers, Inc. All rights reserved.
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Bast, F. (2012). Cancer phylogenetics: Computational modeling of tumor evolution Bioinformatics: Genome Bioinformatics and Computational Biology (pp. 211-230).