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Visualizing tumor evolution with the fishplot package for R

by Mardis, Elaine R. , Miller, Christopher A. , Wilson, Richard K. , Dang, Ha X. , Ley, Timothy J. , McMichael, Joshua , Ding, Li , Maher, Christopher A.

in Animal Genetics and Genomics / Biomedical and Life Sciences / Cancer / Carcinogenesis / Chemotherapy / DNA sequencing / Evolution / Funding / Genetic aspects / Genomes / Genomics / Genomics - methods / Heterogeneity / Human and rodent genomics / Leukemia / Life Sciences / Microarrays / Microbial Genetics and Genomics / Models, Biological / Molecular evolution / Nucleotide sequencing / Plant Genetics and Genomics / Proteomics / Software / Studies / Tumors / Web Browser

2016

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Visualizing tumor evolution with the fishplot package for R

by Mardis, Elaine R. , Miller, Christopher A. , Wilson, Richard K. , Dang, Ha X. , Ley, Timothy J. , McMichael, Joshua , Ding, Li , Maher, Christopher A.

2016

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Visualizing tumor evolution with the fishplot package for R

by Mardis, Elaine R. , Miller, Christopher A. , Wilson, Richard K. , Dang, Ha X. , Ley, Timothy J. , McMichael, Joshua , Ding, Li , Maher, Christopher A.

2016

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Journal Article

Visualizing tumor evolution with the fishplot package for R

Mardis, Elaine R.,

Miller, Christopher A.,

Wilson, Richard K.,

Dang, Ha X.,

Ley, Timothy J.,

McMichael, Joshua,

Ding, Li,

Maher, Christopher A.

2016

Overview

Background Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visualizations, such as scatterplots, can be difficult to interpret. Current data visualization methods are also typically manual and laborious, and often only approximate subclonal fractions. Results We have developed an R package that accurately and intuitively displays changes in clonal structure over time. It requires simple input data and produces illustrative and easy-to-interpret graphs suitable for diagnosis, presentation, and publication. Conclusions The simplicity, power, and flexibility of this tool make it valuable for visualizing tumor evolution, and it has potential utility in both research and clinical settings. The fishplot package is available at https://github.com/chrisamiller/fishplot .

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Publisher

BioMed Central,BioMed Central Ltd,Springer Nature B.V

Subject

Animal Genetics and Genomics

/ Biomedical and Life Sciences

/ Cancer