wANNOVAR: annotating genetic variants for personal genomes via the web

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.

Aldosterone-stimulating somatic gene mutations are common in normal adrenal glands

“…Variants were annotated using Annovar (42). Called variants were filtered to identify potential driving somatic mutations by removing synonymous or noncoding variants and those with frequencies >0.01 in normal populations from Exome Sequencing Project 6500 or 1000 Genomes, flow-corrected read depths <50, flow variant allele-containing reads <10, variant allele fractions (flow variant allele-containing reads/flowcorrected read depths) <0.10, or flow variant allele calling forward to reverse read ratio <0.2 or >5.…”

PI4K2A deficiency in an intellectual disability, epilepsy, myoclonus, akathisia syndrome

“…Base calling and analysis were performed using Illumina HiSeq Analysis Software v2‐2.5.55.1311. Reads were mapped to hg19 using Isaac alignment (SAAC00776.15.01.27) and single nucleotide and small indel variants called Isaac variant caller Starling 2.1.4.2 and annotated as previously described4 based on ANNOVAR 5. Copy number variants were detected as described by Trost et al6 Individuals I‐1, I‐2, II‐4, II‐6, II‐8, and II‐9 were also genotyped using Infinium HumanOmni2.5‐8 BeadChip according to the manufacture's protocol.…”

Whole-Exome Sequencing Reveals TopBP1 as a Novel Gene in Idiopathic Pulmonary Arterial Hypertension

“…Raw sequence reads were aligned to human reference sequence hg19 using SAM/BAM. Sequencing data were analyzed using ANNOVAR software (openbioinformatics.org) (19). After filtering synonymous (i.e., not altering protein sequence) variants and those with estimated minor allele frequency greater than 15%, two independent investigators screened the resulting list for genes predicted to have nonsynonymous (i.e., altering protein sequencing) variants with known heart and lung expression and with association to human disease based on annotation in public databases (GeneCards, KEGG, PubMed, and OMIM).…”

“…After filtering synonymous (i.e., not altering protein sequence) variants and those with estimated minor allele frequency greater than 15%, two independent investigators screened the resulting list for genes predicted to have nonsynonymous (i.e., altering protein sequencing) variants with known heart and lung expression and with association to human disease based on annotation in public databases (GeneCards, KEGG, PubMed, and OMIM). To further estimate the impact of selected variants on protein structure and function we used a set of metrics that take into consideration functional impact on evolutionary conserved domains: Polyphen2 (20), SIFT (21), MutationTaster (21), LRT (22), and GERP (19). All clinically relevant candidate variants were validated using Sanger capillary sequencing methods.…”