Journal Article

The personal genome browser: visualizing functions of genetic variants

Liran Juan, Mingxiang Teng, Tianyi Zang, Yafeng Hao, Zhenxing Wang, Chengwu Yan, Yongzhuang Liu, Jie Li, Tianjiao Zhang and Yadong Wang

in Nucleic Acids Research

Volume 42, issue W1, pages W192-W197
Published in print July 2014 | ISSN: 0305-1048
Published online May 2014 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gku361

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Advances in high-throughput sequencing technologies have brought us into the individual genome era. Projects such as the 1000 Genomes Project have led the individual genome sequencing to become more and more popular. How to visualize, analyse and annotate individual genomes with knowledge bases to support genome studies and personalized healthcare is still a big challenge. The Personal Genome Browser (PGB) is developed to provide comprehensive functional annotation and visualization for individual genomes based on the genetic–molecular–phenotypic model. Investigators can easily view individual genetic variants, such as single nucleotide variants (SNVs), INDELs and structural variations (SVs), as well as genomic features and phenotypes associated to the individual genetic variants. The PGB especially highlights potential functional variants using the PGB built-in method or SIFT/PolyPhen2 scores. Moreover, the functional risks of genes could be evaluated by scanning individual genetic variants on the whole genome, a chromosome, or a cytoband based on functional implications of the variants. Investigators can then navigate to high risk genes on the scanned individual genome. The PGB accepts Variant Call Format (VCF) and Genetic Variation Format (GVF) files as the input. The functional annotation of input individual genome variants can be visualized in real time by well-defined symbols and shapes. The PGB is available at http://www.pgbrowser.org/.

Journal Article.  3302 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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