메뉴 건너뛰기




Volumn 37, Issue 12, 2016, Pages 1272-1282

How to Identify Pathogenic Mutations among All Those Variations: Variant Annotation and Filtration in the Genome Sequencing Era

Author keywords

good practices; high throughput sequencing; pathogenic mutation; variant annotation; variant filtration

Indexed keywords

PROTEIN;

EID: 84992461090     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.23110     Document Type: Review
Times cited : (28)

References (96)
  • 4
    • 77951620816 scopus 로고    scopus 로고
    • An evolutionary approach to the high frequency of the Delta F508 CFTR mutation in European populations
    • Alfonso-Sánchez MA, Pérez-Miranda AM, García-Obregón S, Peña JA. 2010. An evolutionary approach to the high frequency of the Delta F508 CFTR mutation in European populations. Med Hypotheses 74:989–992.
    • (2010) Med Hypotheses , vol.74 , pp. 989-992
    • Alfonso-Sánchez, M.A.1    Pérez-Miranda, A.M.2    García-Obregón, S.3    Peña, J.A.4
  • 5
    • 84946081339 scopus 로고    scopus 로고
    • OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders
    • Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. 2015. OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res 43.D1:D789–D798.
    • (2015) Nucleic Acids Res , vol.43.D1 , pp. D789-D798
    • Amberger, J.S.1    Bocchini, C.A.2    Schiettecatte, F.3    Scott, A.F.4    Hamosh, A.5
  • 8
    • 79959276553 scopus 로고    scopus 로고
    • Deploying whole genome sequencing in clinical practice and public health: meeting the challenge one bin at a time
    • Berg JS, Khoury MJ, Evans JP. 2011. Deploying whole genome sequencing in clinical practice and public health: meeting the challenge one bin at a time. Genet Med 13:499–504.
    • (2011) Genet Med , vol.13 , pp. 499-504
    • Berg, J.S.1    Khoury, M.J.2    Evans, J.P.3
  • 16
    • 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. 2012. Predicting the functional effect of amino acid substitutions and indels. PLoS One 7:e46688.
    • (2012) PLoS One , vol.7
    • Choi, Y.1    Sims, G.E.2    Murphy, S.3    Miller, J.R.4    Chan, A.P.5
  • 17
    • 69749122314 scopus 로고    scopus 로고
    • Identification of deleterious mutations within three human genomes
    • Chun S, Fay JC. 2009. Identification of deleterious mutations within three human genomes. Genome Res 19:1553–1561.
    • (2009) Genome Res , vol.19 , pp. 1553-1561
    • Chun, S.1    Fay, J.C.2
  • 22
    • 84891375981 scopus 로고    scopus 로고
    • Functional anatomy of distant-acting mammalian enhancers
    • 20120359
    • Dickel DE, Visel A, Pennacchio LA. 2013. Functional anatomy of distant-acting mammalian enhancers. Phil. Trans. R. Soc. B 368.1620:20120359.
    • (2013) Phil. Trans. R. Soc. B , vol.368 , Issue.1620
    • Dickel, D.E.1    Visel, A.2    Pennacchio, L.A.3
  • 23
    • 84926430386 scopus 로고    scopus 로고
    • Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies
    • Dong C, Wei P, Jian X, Gibbs R. 2015. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet 24.8:2125–2137.
    • (2015) Hum Mol Genet , vol.24 , Issue.8 , pp. 2125-2137
    • Dong, C.1    Wei, P.2    Jian, X.3    Gibbs, R.4
  • 24
    • 81355142141 scopus 로고    scopus 로고
    • Non-coding RNAs in human disease
    • Esteller M. 2011. Non-coding RNAs in human disease. Nat Rev Genet 12:861–874.
    • (2011) Nat Rev Genet , vol.12 , pp. 861-874
    • Esteller, M.1
  • 26
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194.
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 29
    • 22844452823 scopus 로고    scopus 로고
    • LOVD: easy creation of a locus-specific sequence variation database using an “LSDB-in-a-box” approach
    • Fokkema IFAC, Dunnen den JT, Taschner PEM. 2005. LOVD: easy creation of a locus-specific sequence variation database using an “LSDB-in-a-box” approach. Hum Mutat 26:63–68.
    • (2005) Hum Mutat , vol.26 , pp. 63-68
    • Fokkema, I.F.A.C.1    Dunnen den, J.T.2    Taschner, P.E.M.3
  • 31
    • 66349086264 scopus 로고    scopus 로고
    • Identifying novel constrained elements by exploiting biased substitution patterns
    • Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. 2009. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics 25:54–62.
    • (2009) Bioinformatics , vol.25 , pp. 54-62
    • Garber, M.1    Guttman, M.2    Clamp, M.3    Zody, M.C.4    Friedman, N.5    Xie, X.6
  • 32
    • 84946735654 scopus 로고    scopus 로고
    • Gene Ontology Consortium: going forward
    • Gene Ontology Consortium. 2015. Gene Ontology Consortium: going forward. Nucleic Acids Res 43:D1049–D1056.
    • (2015) Nucleic Acids Res , vol.43 , pp. D1049-D1056
  • 34
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks J, Nekrutenko A, Taylor J, Team G. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11.8:1.
    • (2010) Genome Biol , vol.11 , Issue.8 , pp. 1
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3    Team, G.4
  • 35
    • 79953715693 scopus 로고    scopus 로고
    • Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel
    • González-Pérez A, Lopez-Bigas N. 2011. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet 88:440–449.
    • (2011) Am J Hum Genet , vol.88 , pp. 440-449
    • González-Pérez, A.1    Lopez-Bigas, N.2
  • 36
    • 84878682420 scopus 로고    scopus 로고
    • The Genotype-Tissue Expression (GTEx) project
    • GTEx Consortium. 2013. The Genotype-Tissue Expression (GTEx) project. Nat Genet 45:580–585.
    • (2013) Nat Genet , vol.45 , pp. 580-585
  • 37
    • 84924039302 scopus 로고    scopus 로고
    • A method for calculating probabilities of fitness consequences for point mutations across the human genome
    • Gulko B, Hubisz MJ, Gronau I, Siepel A. 2015. A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat Genet 47:276–283.
    • (2015) Nat Genet , vol.47 , pp. 276-283
    • Gulko, B.1    Hubisz, M.J.2    Gronau, I.3    Siepel, A.4
  • 43
    • 84878825120 scopus 로고    scopus 로고
    • Next generation sequencing for neurological diseases: new hope or new hype?
    • Keogh MJ, Chinnery PF. 2013. Next generation sequencing for neurological diseases: new hope or new hype? Clin Neurol Neurosurg 115:948–953.
    • (2013) Clin Neurol Neurosurg , vol.115 , pp. 948-953
    • Keogh, M.J.1    Chinnery, P.F.2
  • 44
    • 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. 2014. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46.3:310.
    • (2014) Nat Genet , vol.46 , Issue.3 , pp. 310
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 50
    • 84928204559 scopus 로고    scopus 로고
    • wKGGSeq: a comprehensive strategy-based and disease-targeted online framework to facilitate exome sequencing studies of inherited disorders
    • Li MJ, Deng J, Wang P, Yang W, Ho SL, Sham PC, Wang J, Li M. 2015. wKGGSeq: a comprehensive strategy-based and disease-targeted online framework to facilitate exome sequencing studies of inherited disorders. Hum Mutat 36:496–503.
    • (2015) Hum Mutat , vol.36 , pp. 496-503
    • Li, M.J.1    Deng, J.2    Wang, P.3    Yang, W.4    Ho, S.L.5    Sham, P.C.6    Wang, J.7    Li, M.8
  • 51
    • 84957942283 scopus 로고    scopus 로고
    • dbNSFP v3.0: a one-stop database of functional predictions and annotations for human nonsynonymous and splice-site SNVs
    • Liu X, Wu C, Li C, Boerwinkle E. 2016. dbNSFP v3.0: a one-stop database of functional predictions and annotations for human nonsynonymous and splice-site SNVs. Hum Mutat 37:235–241.
    • (2016) Hum Mutat , vol.37 , pp. 235-241
    • Liu, X.1    Wu, C.2    Li, C.3    Boerwinkle, E.4
  • 55
    • 84919687395 scopus 로고    scopus 로고
    • Nonsense-mediated decay in genetic disease: friend or foe? Mutation research
    • Miller JN, Pearce DA. 2014. Nonsense-mediated decay in genetic disease: friend or foe? Mutation research. Rev Mutat Res 762:52–64.
    • (2014) Rev Mutat Res , vol.762 , pp. 52-64
    • Miller, J.N.1    Pearce, D.A.2
  • 57
    • 0344198459 scopus 로고    scopus 로고
    • The spliceosome: the most complex macromolecular machine in the cell?
    • Nilsen TW. 2003. The spliceosome: the most complex macromolecular machine in the cell? Bioessays 25.12:1147–1149.
    • (2003) Bioessays , vol.25 , Issue.12 , pp. 1147-1149
    • Nilsen, T.W.1
  • 60
    • 84880800567 scopus 로고    scopus 로고
    • GEMINI: integrative exploration of genetic variation and genome annotations
    • Paila U, Chapman BA, Kirchner R, Quinlan AR. 2013. GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput Biol 9:e1003153.
    • (2013) PLoS Comput Biol , vol.9
    • Paila, U.1    Chapman, B.A.2    Kirchner, R.3    Quinlan, A.R.4
  • 61
    • 0035282695 scopus 로고    scopus 로고
    • GeneSplicer: a new computational method for splice site prediction
    • Pertea M, Lin X, Salzberg SL. 2001. GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res 29:1185–1190.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1185-1190
    • Pertea, M.1    Lin, X.2    Salzberg, S.L.3
  • 63
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20:110–121.
    • (2010) Genome Res , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 65
    • 84928997067 scopus 로고    scopus 로고
    • DANN: a deep learning approach for annotating the pathogenicity of genetic variants
    • Quang D, Chen Y, Xie X. 2015. DANN: a deep learning approach for annotating the pathogenicity of genetic variants. Bioinformatics 31:761–763.
    • (2015) Bioinformatics , vol.31 , pp. 761-763
    • Quang, D.1    Chen, Y.2    Xie, X.3
  • 67
    • 80053189298 scopus 로고    scopus 로고
    • Predicting the functional impact of protein mutations: application to cancer genomics
    • Reva B, Antipin Y, Sander C. 2011. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 39:e118.
    • (2011) Nucleic Acids Res , vol.39
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 68
    • 84885025223 scopus 로고    scopus 로고
    • RNA pathogenesis via Toll-like receptor-activated inflammation in expanded repeat neurodegenerative diseases
    • Richards RI, Samaraweera SE, van Eyk CL, O'Keefe LV, Suter CM. 2013. RNA pathogenesis via Toll-like receptor-activated inflammation in expanded repeat neurodegenerative diseases. Front Mol Neurosci 6:25.
    • (2013) Front Mol Neurosci , vol.6 , pp. 25
    • Richards, R.I.1    Samaraweera, S.E.2    van Eyk, C.L.3    O'Keefe, L.V.4    Suter, C.M.5
  • 69
    • 84905576523 scopus 로고    scopus 로고
    • Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
    • Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SRF, WGS500 Consortium, Wilkie AOM, McVean G, Lunter G. 2014. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat Genet 46:912–918.
    • (2014) Nat Genet , vol.46 , pp. 912-918
    • Rimmer, A.1    Phan, H.2    Mathieson, I.3    Iqbal, Z.4    Twigg, S.R.F.5    Wilkie, A.O.M.6    McVean, G.7    Lunter, G.8
  • 70
  • 74
    • 84879960888 scopus 로고    scopus 로고
    • The DNA data deluge: fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze
    • Schatz MC, Langmead B. 2013. The DNA data deluge: fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze. IEEE Spectr 50:26–33.
    • (2013) IEEE Spectr , vol.50 , pp. 26-33
    • Schatz, M.C.1    Langmead, B.2
  • 75
    • 84897456458 scopus 로고    scopus 로고
    • MutationTaster2: mutation prediction for the deep-sequencing age
    • Schwarz JM, Cooper DN, Schuelke M, Seelow D. 2014. MutationTaster2: mutation prediction for the deep-sequencing age. Nat Methods 11:361–362.
    • (2014) Nat Methods , vol.11 , pp. 361-362
    • Schwarz, J.M.1    Cooper, D.N.2    Schuelke, M.3    Seelow, D.4
  • 81
  • 84
    • 84857187982 scopus 로고    scopus 로고
    • VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer
    • Teer JK, Green ED, Mullikin JC, Biesecker LG. 2012. VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer. Bioinformatics 28:599–600.
    • (2012) Bioinformatics , vol.28 , pp. 599-600
    • Teer, J.K.1    Green, E.D.2    Mullikin, J.C.3    Biesecker, L.G.4
  • 88
    • 84891783174 scopus 로고    scopus 로고
    • Activities at the Universal Protein Resource (UniProt)
    • UniProt Consortium. 2014. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42:D191–D198.
    • (2014) Nucleic Acids Res , vol.42 , pp. D191-D198
  • 89
    • 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. 38:e164.
    • (2010) , vol.38
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 90
    • 79957840356 scopus 로고    scopus 로고
    • Long noncoding RNAs and human disease
    • Wapinski O, Chang HY. 2011. Long noncoding RNAs and human disease. Trends Cell Biol 21:354–361.
    • (2011) Trends Cell Biol , vol.21 , pp. 354-361
    • Wapinski, O.1    Chang, H.Y.2
  • 91
    • 84976873328 scopus 로고    scopus 로고
    • HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
    • Ward LD, Kellis M. 2016. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res 44:D877–D881.
    • (2016) Nucleic Acids Res , vol.44 , pp. D877-D881
    • Ward, L.D.1    Kellis, M.2
  • 92
    • 84940611109 scopus 로고    scopus 로고
    • Phenolyzer: phenotype-based prioritization of candidate genes for human diseases
    • Yang H, Robinson PN, Wang K. 2015. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. Nat Methods 12:841–843.
    • (2015) Nat Methods , vol.12 , pp. 841-843
    • Yang, H.1    Robinson, P.N.2    Wang, K.3
  • 95
    • 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. J Comput Biol 11:377–394.
    • (2004) J Comput Biol , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 96
    • 84924333321 scopus 로고    scopus 로고
    • A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
    • Zhao S, Zhang B. 2015. A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification. BMC Genomics 16:97.
    • (2015) BMC Genomics , vol.16 , pp. 97
    • Zhao, S.1    Zhang, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.