메뉴 건너뛰기




Volumn 19, Issue 1, 2018, Pages

The VAAST Variant Prioritizer (VVP): Ultrafast, easy to use whole genome variant prioritization tool

Author keywords

Genomics; Human genome; Variant prioritization; Variants of uncertain significance

Indexed keywords

CLINICAL RESEARCH; DIAGNOSIS;

EID: 85042543566     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-018-2056-y     Document Type: Article
Times cited : (24)

References (33)
  • 1
    • 80051968181 scopus 로고    scopus 로고
    • Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
    • Cooper GM, Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet. 2011;12:628-40. https://doi.org/10.1038/nrg3046. PMID: 21850043
    • (2011) Nat Rev Genet , vol.12 , pp. 628-640
    • Cooper, G.M.1    Shendure, J.2
  • 2
    • 85029470345 scopus 로고    scopus 로고
    • Settling the score: variant prioritization and Mendelian disease
    • PMID: 28804138.
    • Eilbeck K, Quinlan A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet. 2017; https://doi.org/10.1038/nrg.2017.52. PMID: 28804138
    • (2017) Nat Rev Genet
    • Eilbeck, K.1    Quinlan, A.2    Yandell, M.3
  • 3
    • 33750353461 scopus 로고    scopus 로고
    • Predicting the effects of amino acid substitutions on protein function
    • Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet. 2006;7:61-80. https://doi.org/10.1146/annurev.genom.7.080505.115630. PMID: 28747718
    • (2006) Annu Rev Genomics Hum Genet , vol.7 , pp. 61-80
    • Ng, P.C.1    Henikoff, S.2
  • 5
    • 84928209346 scopus 로고    scopus 로고
    • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology
    • Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, Committee, ALQA. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405-24. https://doi.org/10.1038/gim.2015.30. PMCID: PMC4544753
    • (2015) Genet Med , vol.17 , pp. 405-424
    • Richards, S.1    Aziz, N.2    Bale, S.3    Bick, D.4    Das, S.5    Gastier-Foster, J.6    Grody, W.W.7    Hegde, M.8    Lyon, E.9    Spector, E.10    Voelkerding, K.11    Rehm, H.L.12
  • 6
    • 85042522050 scopus 로고    scopus 로고
    • NHS Guidelines: https://www.nice.org.uk/guidance.
  • 10
    • 84904006087 scopus 로고    scopus 로고
    • Rare-variant association analysis: study designs and statistical tests
    • Lee S, Abecasis GR, Boehnke M, Lin X. Rare-variant association analysis: study designs and statistical tests. Am J Hum Genet. 2014;95:5-23. https://doi.org/10.1016/j.ajhg.2014.06.009. PMCID: PMC4085641
    • (2014) Am J Hum Genet , vol.95 , pp. 5-23
    • Lee, S.1    Abecasis, G.R.2    Boehnke, M.3    Lin, X.4
  • 11
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310-5. https://doi.org/10.1038/ng.2892. PMCID: PMC3992975
    • (2014) Nat Genet , vol.46 , pp. 310-315
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 12
    • 85042539875 scopus 로고    scopus 로고
    • dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/.
  • 14
    • 84881609951 scopus 로고    scopus 로고
    • VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix
    • Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M. VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. Genet Epidemiol. 2013;37:622-34. https://doi.org/10.1002/gepi.21743. PMCID: PMC3791556
    • (2013) Genet Epidemiol , vol.37 , pp. 622-634
    • Hu, H.1    Huff, C.D.2    Moore, B.3    Flygare, S.4    Reese, M.G.5    Yandell, M.6
  • 17
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073-81. https://doi.org/10.1038/nprot.2009.86.
    • (2009) Nat Protoc , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 21
    • 77955405475 scopus 로고    scopus 로고
    • Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor
    • McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor. Bioinformatics. 2010;26:2069-70. https://doi.org/10.1093/bioinformatics/btq330. PMCID: PMC2916720
    • (2010) Bioinformatics , vol.26 , pp. 2069-2070
    • McLaren, W.1    Pritchard, B.2    Rios, D.3    Chen, Y.4    Flicek, P.5    Cunningham, F.6
  • 22
    • 0028813337 scopus 로고
    • A space-time process model for the evolution of DNA sequences
    • Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995;139:993-1005. PMCID: PMC1206396
    • (1995) Genetics , vol.139 , pp. 993-1005
    • Yang, Z.1
  • 23
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992;89:10915-9. PMCID: PMC50453
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 25
    • 84867301515 scopus 로고    scopus 로고
    • Predicting the functional effect of amino acid substitutions and indels
    • Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. PLoS One. 2012;7:e46688. https://doi.org/10.1371/journal.pone.0046688. PMCID: PMC3466303
    • (2012) PLoS One , vol.7
    • Choi, Y.1    Sims, G.E.2    Murphy, S.3    Miller, J.R.4    Chan, A.P.5
  • 29
    • 85042551430 scopus 로고    scopus 로고
    • Phevor2: http://weatherby.genetics.utah.edu/phevor2/index.html.
  • 30
    • 85000623648 scopus 로고    scopus 로고
    • CADD score has limited clinical validity for the identification of pathogenic variants in noncoding regions in a hereditary cancer panel
    • Mather CA, Mooney SD, Salipante SJ, Scroggins S, Wu D, Pritchard CC, Shirts BH. CADD score has limited clinical validity for the identification of pathogenic variants in noncoding regions in a hereditary cancer panel. Genet Med. 2016;18:1269-75. https://doi.org/10.1038/gim.2016.44. PMCID: PMC5097698
    • (2016) Genet Med , vol.18 , pp. 1269-1275
    • Mather, C.A.1    Mooney, S.D.2    Salipante, S.J.3    Scroggins, S.4    Wu, D.5    Pritchard, C.C.6    Shirts, B.H.7
  • 31
    • 16244366026 scopus 로고
    • Index for rating diagnostic tests
    • Youden WJ. Index for rating diagnostic tests. Cancer. 1950;3:32-5. PMCID
    • (1950) Cancer , vol.3 , pp. 32-35
    • Youden, W.J.1
  • 32
    • 85042522631 scopus 로고    scopus 로고
    • Illumina Platinum Genomes: https://www.illumina.com/platinumgenomes.html.
  • 33
    • 0028062781 scopus 로고
    • Cystic fibrosis heterozygote resistance to cholera toxin in the cystic fibrosis mouse model
    • Gabriel SE, Brigman KN, Koller BH, Boucher RC, Stutts MJ. Cystic fibrosis heterozygote resistance to cholera toxin in the cystic fibrosis mouse model. Science. 1994;266:107-9.
    • (1994) Science , vol.266 , pp. 107-109
    • Gabriel, S.E.1    Brigman, K.N.2    Koller, B.H.3    Boucher, R.C.4    Stutts, M.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.