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wANNOVAR: annotating genetic variants for personal genomes via the web
  1. Xiao Chang1,
  2. Kai Wang1,2
  1. 1Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
  2. 2Department of Psychiatry and Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
  1. Correspondence to Dr Kai Wang, University of Southern California, 1501 San Pablo St, Los Angeles, CA 90089, USA; kaiwang{at}usc.edu

Abstract

Background High-throughput DNA sequencing platforms have become widely available. As a result, personal genomes are increasingly being sequenced in research and clinical settings. However, the resulting massive amounts of variants data pose significant challenges to the average biologists and clinicians without bioinformatics skills.

Methods and results We developed a web server called wANNOVAR to address the critical needs for functional annotation of genetic variants from personal genomes. The server provides simple and intuitive interface to help users determine the functional significance of variants. These include annotating single nucleotide variants and insertions/deletions for their effects on genes, reporting their conservation levels (such as PhyloP and GERP++ scores), calculating their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieving allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 5400 exomes), and implementing a ‘variants reduction’ protocol to identify a subset of potentially deleterious variants/genes. We illustrated how wANNOVAR can help draw biological insights from sequencing data, by analysing genetic variants generated on two Mendelian diseases.

Conclusions We conclude that wANNOVAR will help biologists and clinicians take advantage of the personal genome information to expedite scientific discoveries. The wANNOVAR server is available at http://wannovar.usc.edu, and will be continuously updated to reflect the latest annotation information.

  • Mendelian diseases
  • genetic variation
  • functional annotation
  • ANNOVAR
  • disease mutation

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Footnotes

  • Funding The study is supported by start-up funds from the Zilkha Neurogenetic Institute and grant number HG006465 from NIH/NHGRI (K.W.).

  • Competing interests None.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data sharing statement The two data sets used in the manuscript are available to users in the “Example” section of the wANNOVAR server.

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