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Volumn 2015, Issue 3, 2015, Pages

VaRank: A simple and powerful tool for ranking genetic variants

Author keywords

Annotation; Barcode; Human genetics; Molecular diagnostic; Mutation detection; Next generation sequencing; Software; Variant ranking

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; BARDET BIEDL SYNDROME; BIOINFORMATICS; COMPUTER PROGRAM; DNA BARCODING; GENE IDENTIFICATION; GENE MUTATION; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENETICS; INFORMATION PROCESSING; INTELLECTUAL IMPAIRMENT; MOLECULAR DIAGNOSIS; MOLECULAR GENETICS; PATHOGENICITY;

EID: 84926483364     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.796     Document Type: Article
Times cited : (71)

References (43)
  • 3
    • 84907500717 scopus 로고    scopus 로고
    • Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing
    • Bao R, Huang L, Andrade J, Tan W, Kibbe WA, Jiang H, Feng G. 2014. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Informatics 13:67-82 DOI 10.4137/CIN.S13779.
    • (2014) Cancer Informatics , vol.13 , pp. 67-82
    • Bao, R.1    Huang, L.2    Andrade, J.3    Tan, W.4    Kibbe, W.A.5    Jiang, H.6    Feng, G.7
  • 4
    • 84899967710 scopus 로고    scopus 로고
    • A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i)
    • Bermejo-Das-Neves C, Nguyen HN, Poch O, Thompson JD. 2014. A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). BMC Bioinformatics 15:111 DOI 10.1186/1471-2105-15-111.
    • (2014) BMC Bioinformatics , vol.15 , pp. 111
    • Bermejo-Das-Neves, C.1    Nguyen, H.N.2    Poch, O.3    Thompson, J.D.4
  • 5
    • 64749099749 scopus 로고    scopus 로고
    • Role of 5'- and 3'-untranslated regions of mRNAs in human diseases
    • Chatterjee S, Pal JK. 2009. Role of 5'- and 3'-untranslated regions of mRNAs in human diseases. Biology of the Cell 101:251-262 DOI 10.1042/BC20080104.
    • (2009) Biology of the Cell , vol.101 , pp. 251-262
    • Chatterjee, S.1    Pal, J.K.2
  • 6
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
    • Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6:80-92 DOI 10.4161/fly.19695.
    • (2012) Fly (Austin) , vol.6 , pp. 80-92
    • Cingolani, P.1    Platts, A.2    Wang le, L.3    Coon, M.4    Nguyen, T.5    Wang, L.6    Land, S.J.7    Lu, X.8    Ruden, D.M.9
  • 7
    • 77952574849 scopus 로고    scopus 로고
    • Uncovering the roles of rare variants in common disease through whole-genome sequencing
    • Cirulli ET, Goldstein DB. 2010. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nature Reviews Genetics 11:415-425 DOI 10.1038/nrg2779.
    • (2010) Nature Reviews Genetics , vol.11 , pp. 415-425
    • Cirulli, E.T.1    Goldstein, D.B.2
  • 10
    • 77955868835 scopus 로고    scopus 로고
    • Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations
    • Flanagan SE, Patch AM, Ellard S. 2010. Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations. Genetic Testing and Molecular Biomarkers 14:533-537 DOI 10.1089/gtmb.2010.0036.
    • (2010) Genetic Testing and Molecular Biomarkers , vol.14 , pp. 533-537
    • Flanagan, S.E.1    Patch, A.M.2    Ellard, S.3
  • 11
    • 80051688000 scopus 로고    scopus 로고
    • Field guide to next-generation DNA sequencers
    • Glenn TC. 2011. Field guide to next-generation DNA sequencers. Molecular Ecology Resources 11:759-769 DOI 10.1111/j.1755-0998.2011.03024.x.
    • (2011) Molecular Ecology Resources , vol.11 , pp. 759-769
    • Glenn, T.C.1
  • 12
    • 79957621519 scopus 로고    scopus 로고
    • Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed
    • Hicks S, Wheeler DA, Plon SE, Kimmel M. 2011. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Human Mutation 32:661-668 DOI 10.1002/humu.21490.
    • (2011) Human Mutation , vol.32 , pp. 661-668
    • Hicks, S.1    Wheeler, D.A.2    Plon, S.E.3    Kimmel, M.4
  • 14
    • 84862777146 scopus 로고    scopus 로고
    • Predicting the effects of frameshifting indels
    • Hu J, Ng P. 2012. Predicting the effects of frameshifting indels. Genome Biology 13:R9 DOI 10.1186/gb-2012-13-2-r9.
    • (2012) Genome Biology , vol.13 , pp. R9
    • Hu, J.1    Ng, P.2
  • 15
    • 84926503617 scopus 로고    scopus 로고
    • In silico prediction of splice-altering single nucleotide variants in the human genome
    • Jian X, Boerwinkle E, Liu X. 2014. In silico prediction of splice-altering single nucleotide variants in the human genome. Nucleic Acids Research 42:13534-13544 DOI 10.1093/nar/gku1206.
    • (2014) Nucleic Acids Research , vol.42 , pp. 13534-13544
    • Jian, X.1    Boerwinkle, E.2    Liu, X.3
  • 16
    • 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. 2009. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols 4:1073-1081 DOI 10.1038/nprot.2009.86.
    • (2009) Nature Protocols , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 20
    • 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. 2010. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26:2069-2070 DOI 10.1093/bioinformatics/btq330.
    • (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
  • 32
    • 0023651307 scopus 로고
    • RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression
    • Shapiro MB, Senapathy P. 1987. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Research 15:7155-7174 DOI 10.1093/nar/15.17.7155.
    • (1987) Nucleic Acids Research , vol.15 , pp. 7155-7174
    • Shapiro, M.B.1    Senapathy, P.2
  • 37
    • 84891837451 scopus 로고    scopus 로고
    • The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine
    • Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. 2014. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genetics 133:1-9 DOI 10.1007/s00439-013-1358-4.
    • (2014) Human Genetics , vol.133 , pp. 1-9
    • Stenson, P.D.1    Mort, M.2    Ball, E.V.3    Shaw, K.4    Phillips, A.5    Cooper, D.N.6
  • 38
    • 79955001682 scopus 로고    scopus 로고
    • Describing structural changes by extending HGVS sequence variation nomenclature
    • Taschner PE, den Dunnen JT. 2011. Describing structural changes by extending HGVS sequence variation nomenclature. Human Mutation 32:507-511 DOI 10.1002/humu.21427.
    • (2011) Human Mutation , vol.32 , pp. 507-511
    • Taschner, P.E.1    den Dunnen, J.T.2
  • 39
    • 55549145156 scopus 로고    scopus 로고
    • In silico analysis of missense substitutions using sequence-alignment based methods
    • Tavtigian SV, Greenblatt MS, Lesueur F, Byrnes GB, Variants IUG. 2008. In silico analysis of missense substitutions using sequence-alignment based methods. Human Mutation 29:1327-1336 DOI 10.1002/humu.20892.
    • (2008) Human Mutation , vol.29 , pp. 1327-1336
    • Tavtigian, S.V.1    Greenblatt, M.S.2    Lesueur, F.3    Byrnes, G.B.4    Variants, I.U.G.5
  • 41
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    • Wang K, Li M, Hakonarson H. 2010. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38:e164 DOI 10.1093/nar/gkq603.
    • (2010) Nucleic Acids Research , vol.38 , pp. e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 42
    • 84898852770 scopus 로고    scopus 로고
    • SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences
    • Wong K-C, Zhang Z. 2014. SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences. Bioinformatics 30:1112-1119 DOI 10.1093/bioinformatics/btt769.
    • (2014) Bioinformatics , vol.30 , pp. 1112-1119
    • Wong, K.-C.1    Zhang, Z.2
  • 43
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • Yeo G, Burge CB. 2004. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. Journal of Computational Biology 11:377-394 DOI 10.1089/1066527041410418.
    • (2004) Journal of Computational Biology , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.