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The personal genome browser: visualizing functions of genetic variants
Liran Juan1, Mingxiang Teng1, Tianyi Zang1
1Center for Bioinformatics, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
Nucleic Acids Research
|May 7, 2014
Summary
The Personal Genome Browser (PGB) visualizes and annotates individual genomes, aiding personalized healthcare. It analyzes genetic variants and highlights potential functional risks for genome studies.
Area of Science:
- Genomics
- Bioinformatics
- Personalized Medicine
Background:
- High-throughput sequencing enables individual genome analysis.
- Visualizing and annotating individual genomes presents challenges for research and healthcare.
- Existing tools lack comprehensive functional annotation and visualization.
Purpose of the Study:
- To develop a tool for comprehensive functional annotation and visualization of individual genomes.
- To support genome studies and personalized healthcare by integrating genetic data with knowledge bases.
- To facilitate the identification and analysis of genetic variants and their associated phenotypes.
Main Methods:
- Developed the Personal Genome Browser (PGB) based on a genetic-molecular-phenotypic model.
- Implemented visualization of single nucleotide variants (SNVs), INDELs, and structural variations (SVs).
- Integrated functional annotation using built-in methods and external scores (SIFT/PolyPhen2).
- Enabled real-time visualization of functional annotation for input genome variants.
- Accepted Variant Call Format (VCF) and Genetic Variation Format (GVF) files.
Main Results:
- PGB provides comprehensive functional annotation and visualization for individual genomes.
- Investigators can view genetic variants, genomic features, and associated phenotypes.
- Potential functional variants are highlighted, and functional risks of genes can be evaluated.
- Users can navigate to high-risk genes within the individual genome.
Conclusions:
- PGB addresses the challenge of visualizing and analyzing individual genomes.
- The tool supports genome studies and personalized healthcare by providing functional insights.
- PGB facilitates the interpretation of genetic variants and their implications.
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