wANNOVAR: annotating genetic variants for personal genomes via the web

By Xiao-Xia Chang, Kai Wang. Journal of Medical Genetics, 2012

425 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/df137ecc497ac19475831bf44e3166af8b6e453f

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Eric Boerwinkle
2. Kai Wang
3. Xiaoming Liu
4. Xueqiu Jian
5. Hui Yang
6. B. Feng
7. Chunlei Wu
8. Chang Li

In Molecular Biology

1. Eric Boerwinkle
2. Xiaoming Liu
3. Kai Wang
4. Xueqiu Jian
5. Hui Yang
6. Abhishek Niroula
7. Mauno Vihinen
8. B. Feng

Citations in the corpus

• Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR (2015, methodology): “To facilitate convenient and fast access to ANNOVAR for researchers who prefer a graphical user interface, we have developed a web server called wANNOVAR 26 (http://wannovar.usc. edu), implementing the most commonly used functionalities of ANNOVAR for human genomes in a web interface.”
• dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations (2013, methodology): “It has been recommended by the Faculty of 1000 and adopted by various software (e.g. Lindenbaum et al. 2011; Li et al. 2012; San Lucas et al. 2012; Chang and Wang 2012; Sifrim et al. 2012; Zhang et al. 2013) and databases (e.g. Li et al. 2011).”