Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine

Concise visualization is critical to present large amounts of information in a minimal space that can be interpreted quickly. Clinical applications in precision medicine present an important use case due to the time dependent nature of the interpretations, although visualization is increasingly nece...

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Bibliographic Details
Published in:PloS one 2016-08, Vol.11 (8), p.e0160519-e0160519
Main Authors: Jay, Jeremy J, Brouwer, Cory
Format: Article
Language:English
Subjects:
Automation
Bioinformatics
Biology and Life Sciences
Cancer
Computational Biology
Computer and Information Sciences
Computer programs
Computer security
Cybersecurity
Data integration
Design
DNA methylation
DNA sequencing
Engineering and Technology
Genomics
Humans
Internet
Internet resources
Laboratories
Medicine
Mutation
Pipelines
Precision Medicine
Problem solving
Proteins
Research and Analysis Methods
Security
Software
Therapeutic applications
User-Computer Interface
Visualization
Websites
Workflow
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Description
Summary:Concise visualization is critical to present large amounts of information in a minimal space that can be interpreted quickly. Clinical applications in precision medicine present an important use case due to the time dependent nature of the interpretations, although visualization is increasingly necessary across the life sciences. In this paper we describe the Lollipops software for the presentation of panel or exome sequencing results. Source code and binaries are freely available at https://github.com/pbnjay/lollipops. Although other software and web resources exist to produce lollipop diagrams, these packages are less suited to clinical applications. The demands of precision medicine require the ability to easily fit into a workflow and incorporate external information without manual intervention. The Lollipops software provides a simple command line interface that only requires an official gene symbol and mutation list making it easily scriptable. External information is integrated using the publicly available Uniprot and Pfam resources. Heuristics are used to select the most informative components and condense them for a concise plot. The output is a flexible Scalable Vector Graphic (SVG) diagram that can be displayed in a web page or graphic illustration tool. The Lollipops software creates information-dense, publication-quality mutation plots for automated pipelines and high-throughput workflows in precision medicine. The automatic data integration enables clinical data security, and visualization heuristics concisely present knowledge with minimal user configuration.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0160519