publication . Article . Other literature type . 2010

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

Mingyao Li; Hakon Hakonarson; Kai Wang;
Open Access English
  • Published: 03 Jul 2010 Journal: Nucleic Acids Research, volume 38, issue 16, pages e164-e164 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press
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 co...
Subjects
free text keywords: Methods Online, Genomics, Human genome, Genome browser, Genetics, dbSNP, SNP annotation, Biology, Variant Call Format, 1000 Genomes Project, Exome sequencing
Funded by
NIH| Developing Statistical Methods for Disease Gene Discovery
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01HG004517-01A1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NIH| CTSA INFRASTRUCTURE FOR AIDS RESEARCH
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1UL1RR025774-01
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
21 references, page 1 of 2

Trapnell, C, Salzberg, SL. How to map billions of short reads onto genomes. Nat. Biotechnol.. 2009; 27: 455-457 [OpenAIRE] [PubMed]

Dalca, AV, Brudno, M. Genome variation discovery with high-throughput sequencing data. Brief. Bioinform.. 2010; 11: 3-14 [OpenAIRE] [PubMed]

Ng, SB, Buckingham, KJ, Lee, C, Bigham, AW, Tabor, HK, Dent, KM, Huff, CD, Shannon, PT, Jabs, EW, Nickerson, DA. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet.. 2010; 42: 30-35 [OpenAIRE] [PubMed]

Gamazon, ER, Zhang, W, Konkashbaev, A, Duan, S, Kistner, EO, Nicolae, DL, Dolan, ME, Cox, NJ. SCAN: SNP and copy number annotation. Bioinformatics. 2010; 26: 259-262 [OpenAIRE] [PubMed]

Li, S, Ma, L, Li, H, Vang, S, Hu, Y, Bolund, L, Wang, J. Snap: an integrated SNP annotation platform. Nucleic Acids Res.. 2007; 35: D707-D710 [OpenAIRE] [PubMed]

Ge, D, Zhang, K, Need, AC, Martin, O, Fellay, J, Urban, TJ, Telenti, A, Goldstein, DB. WGAViewer: software for genomic annotation of whole genome association studies. Genome Res.. 2008; 18: 640-643 [OpenAIRE] [PubMed]

Karchin, R. Next generation tools for the annotation of human SNPs. Brief. Bioinform.. 2009; 10: 35-52 [OpenAIRE] [PubMed]

Lee, PH, Shatkay, H. F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res.. 2008; 36: D820-D824 [OpenAIRE] [PubMed]

Ng, PC, Henikoff, S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res.. 2003; 31: 3812-3814 [OpenAIRE] [PubMed]

Ramensky, V, Bork, P, Sunyaev, S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res.. 2002; 30: 3894-3900 [OpenAIRE] [PubMed]

Ng, SB, Turner, EH, Robertson, PD, Flygare, SD, Bigham, AW, Lee, C, Shaffer, T, Wong, M, Bhattacharjee, A, Eichler, EE. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009; 461: 272-276 [OpenAIRE] [PubMed]

Rhead, B, Karolchik, D, Kuhn, RM, Hinrichs, AS, Zweig, AS, Fujita, PA, Diekhans, M, Smith, KE, Rosenbloom, KR, Raney, BJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Res.. 2010; 38: D613-D619 [OpenAIRE] [PubMed]

Curwen, V, Eyras, E, Andrews, TD, Clarke, L, Mongin, E, Searle, SM, Clamp, M. The Ensembl automatic gene annotation system. Genome Res.. 2004; 14: 942-950 [OpenAIRE] [PubMed]

Bentley, DR, Balasubramanian, S, Swerdlow, HP, Smith, GP, Milton, J, Brown, CG, Hall, KP, Evers, DJ, Barnes, CL, Bignell, HR. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008; 456: 53-59 [OpenAIRE] [PubMed]

Pruitt, KD, Tatusova, T, Maglott, DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res.. 2007; 35: D61-D65 [OpenAIRE] [PubMed]

21 references, page 1 of 2
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 co...
Subjects
free text keywords: Methods Online, Genomics, Human genome, Genome browser, Genetics, dbSNP, SNP annotation, Biology, Variant Call Format, 1000 Genomes Project, Exome sequencing
Funded by
NIH| Developing Statistical Methods for Disease Gene Discovery
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01HG004517-01A1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NIH| CTSA INFRASTRUCTURE FOR AIDS RESEARCH
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1UL1RR025774-01
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
21 references, page 1 of 2

Trapnell, C, Salzberg, SL. How to map billions of short reads onto genomes. Nat. Biotechnol.. 2009; 27: 455-457 [OpenAIRE] [PubMed]

Dalca, AV, Brudno, M. Genome variation discovery with high-throughput sequencing data. Brief. Bioinform.. 2010; 11: 3-14 [OpenAIRE] [PubMed]

Ng, SB, Buckingham, KJ, Lee, C, Bigham, AW, Tabor, HK, Dent, KM, Huff, CD, Shannon, PT, Jabs, EW, Nickerson, DA. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet.. 2010; 42: 30-35 [OpenAIRE] [PubMed]

Gamazon, ER, Zhang, W, Konkashbaev, A, Duan, S, Kistner, EO, Nicolae, DL, Dolan, ME, Cox, NJ. SCAN: SNP and copy number annotation. Bioinformatics. 2010; 26: 259-262 [OpenAIRE] [PubMed]

Li, S, Ma, L, Li, H, Vang, S, Hu, Y, Bolund, L, Wang, J. Snap: an integrated SNP annotation platform. Nucleic Acids Res.. 2007; 35: D707-D710 [OpenAIRE] [PubMed]

Ge, D, Zhang, K, Need, AC, Martin, O, Fellay, J, Urban, TJ, Telenti, A, Goldstein, DB. WGAViewer: software for genomic annotation of whole genome association studies. Genome Res.. 2008; 18: 640-643 [OpenAIRE] [PubMed]

Karchin, R. Next generation tools for the annotation of human SNPs. Brief. Bioinform.. 2009; 10: 35-52 [OpenAIRE] [PubMed]

Lee, PH, Shatkay, H. F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res.. 2008; 36: D820-D824 [OpenAIRE] [PubMed]

Ng, PC, Henikoff, S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res.. 2003; 31: 3812-3814 [OpenAIRE] [PubMed]

Ramensky, V, Bork, P, Sunyaev, S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res.. 2002; 30: 3894-3900 [OpenAIRE] [PubMed]

Ng, SB, Turner, EH, Robertson, PD, Flygare, SD, Bigham, AW, Lee, C, Shaffer, T, Wong, M, Bhattacharjee, A, Eichler, EE. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009; 461: 272-276 [OpenAIRE] [PubMed]

Rhead, B, Karolchik, D, Kuhn, RM, Hinrichs, AS, Zweig, AS, Fujita, PA, Diekhans, M, Smith, KE, Rosenbloom, KR, Raney, BJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Res.. 2010; 38: D613-D619 [OpenAIRE] [PubMed]

Curwen, V, Eyras, E, Andrews, TD, Clarke, L, Mongin, E, Searle, SM, Clamp, M. The Ensembl automatic gene annotation system. Genome Res.. 2004; 14: 942-950 [OpenAIRE] [PubMed]

Bentley, DR, Balasubramanian, S, Swerdlow, HP, Smith, GP, Milton, J, Brown, CG, Hall, KP, Evers, DJ, Barnes, CL, Bignell, HR. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008; 456: 53-59 [OpenAIRE] [PubMed]

Pruitt, KD, Tatusova, T, Maglott, DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res.. 2007; 35: D61-D65 [OpenAIRE] [PubMed]

21 references, page 1 of 2
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