Jul 6, 2010

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

Nucleic Acids Research
Kai WangHakon Hakonarson

Abstract

High-throughput sequencing platforms are generating massive amounts of genetic variation data for diverse genomes, but it remains a challenge to pinpoint a small subset of functionally important variants. To fill these unmet needs, we developed the ANNOVAR tool to annotate single nucleotide variants (SNVs) and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP. ANNOVAR can utilize annotation databases from the UCSC Genome Browser or any annotation data set conforming to Generic Feature Format version 3 (GFF3). We also illustrate a 'variants reduction' protocol on 4.7 million SNVs and indels from a human genome, including two causal mutations for Miller syndrome, a rare recessive disease. Through a stepwise procedure, we excluded variants that are unlikely to be causal, and identified 20 candidate genes including the causal gene. Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human g...Continue Reading

  • References21
  • Citations2921

Mentioned in this Paper

Chromosome 11p Deletion Syndrome
Genee-Wiedemann Syndrome
Cytogenetics
Genome
Candidate Disease Gene
Single Nucleotide Polymorphism Database
Computer Programs and Programming
Genomics
Sequencing
Sequence Determinations, DNA

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