메뉴 건너뛰기




Volumn 37, Issue 10, 2016, Pages 1013-1024

The Complementarity Between Protein-Specific and General Pathogenicity Predictors for Amino Acid Substitutions

Author keywords

amino acid variants; in silico pathogenicity predictions; missense variants; molecular diagnostics; next generation sequencing

Indexed keywords

PROTEIN;

EID: 84987753776     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.23048     Document Type: Article
Times cited : (41)

References (61)
  • 1
    • 84989861282 scopus 로고    scopus 로고
    • Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations
    • [Epub ahead of print]
    • Adebali O, Reznik AO, Ory DS, Zhulin IB. 2016. Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations. Genet Med. doi:10.1038/gim.2015.208 [Epub ahead of print]
    • (2016) Genet Med
    • Adebali, O.1    Reznik, A.O.2    Ory, D.S.3    Zhulin, I.B.4
  • 3
    • 84858205858 scopus 로고    scopus 로고
    • Classification of mismatch repair gene missense variants with PON-MMR
    • Ali, H., Olatubosun, A., Vihinen, M. (2012). Classification of mismatch repair gene missense variants with PON-MMR. Hum Mutat 33:642–650.
    • (2012) Hum Mutat , vol.33 , pp. 642-650
    • Ali, H.1    Olatubosun, A.2    Vihinen, M.3
  • 5
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: an overview
    • Baldi, P, Brunak, S, Chauvin, Y, Andersen, CAF, Nielsen, H. 2000. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16:412–424.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.F.4    Nielsen, H.5
  • 8
    • 20544433165 scopus 로고
    • van der Waals volumes and radii
    • Bondi, A. (1964). van der Waals volumes and radii. J Phys Chem 68:441–451.
    • (1964) J Phys Chem , vol.68 , pp. 441-451
    • Bondi, A.1
  • 10
    • 69549111112 scopus 로고    scopus 로고
    • Correlating protein function and stability through the analysis of single amino acid substitutions
    • Bromberg Y, Rost B. 2009. Correlating protein function and stability through the analysis of single amino acid substitutions. BMC Bioinformatics 8(10 Suppl):S8.
    • (2009) BMC Bioinformatics , vol.8 , Issue.10 , pp. 8
    • Bromberg, Y.1    Rost, B.2
  • 11
    • 67749137351 scopus 로고    scopus 로고
    • Functional annotations improve the predictive score of human disease-related mutations in proteins
    • Calabrese, R., Capriotti, E., Fariselli, P., Martelli, P. L., Casadio, R. (2009). Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat 30:1237–1244.
    • (2009) Hum Mutat , vol.30 , pp. 1237-1244
    • Calabrese, R.1    Capriotti, E.2    Fariselli, P.3    Martelli, P.L.4    Casadio, R.5
  • 12
    • 27544469800 scopus 로고    scopus 로고
    • Predicting protein stability changes from sequences using support vector machines
    • Capriotti, E., Fariselli, P., Calabrese, R., Casadio, R. (2005). Predicting protein stability changes from sequences using support vector machines. Bioinformatics 21:ii54–ii58.
    • (2005) Bioinformatics , vol.21 , pp. ii54-ii58
    • Capriotti, E.1    Fariselli, P.2    Calabrese, R.3    Casadio, R.4
  • 15
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 16
    • 0000484499 scopus 로고
    • Hydrophobic parameters of amino acid side-chains from the partitioning of N-acetyl-amino-acid amides
    • Fauchère, J., Pliska, V. (1983). Hydrophobic parameters of amino acid side-chains from the partitioning of N-acetyl-amino-acid amides. Eur J Med Chem-Chim Ther 18:369–375.
    • (1983) Eur J Med Chem-Chim Ther , vol.18 , pp. 369-375
    • Fauchère, J.1    Pliska, V.2
  • 17
    • 84904847752 scopus 로고    scopus 로고
    • MutaCYP: classification of missense mutations in human cytochromes P450
    • Fechter, K., Porollo, A. (2014). MutaCYP: classification of missense mutations in human cytochromes P450. BMC Med Genomics 7:47.
    • (2014) BMC Med Genomics , vol.7 , pp. 47
    • Fechter, K.1    Porollo, A.2
  • 18
    • 10344242920 scopus 로고    scopus 로고
    • Sequence-based prediction of pathological mutations
    • Ferrer-Costa, C., Orozco, M., de la Cruz, X. (2004). Sequence-based prediction of pathological mutations. Proteins 57:811–819.
    • (2004) Proteins , vol.57 , pp. 811-819
    • Ferrer-Costa, C.1    Orozco, M.2    de la Cruz, X.3
  • 19
    • 3042842115 scopus 로고    scopus 로고
    • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
    • Fodor, A. A., Aldrich, R. W. (2004). Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 56:211–221.
    • (2004) Proteins , vol.56 , pp. 211-221
    • Fodor, A.A.1    Aldrich, R.W.2
  • 20
    • 79953715693 scopus 로고    scopus 로고
    • Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel
    • González-Pérez, A., López-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    López-Bigas, N.2
  • 23
    • 85047688149 scopus 로고    scopus 로고
    • News from the protein mutability landscape
    • Hecht, M, Bromberg, Y, Rost, B. 2013. News from the protein mutability landscape. J Mol Biol 425:3937–3948.
    • (2013) J Mol Biol , vol.425 , pp. 3937-3948
    • Hecht, M.1    Bromberg, Y.2    Rost, B.3
  • 24
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S., Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915–10919.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 25
    • 84865795096 scopus 로고    scopus 로고
    • Prioritization of pathogenic mutations in the protein kinase superfamily
    • Izarzugaza, J. M. G., Pozo, A del, Vazquez, M., Valencia, A. (2012). Prioritization of pathogenic mutations in the protein kinase superfamily. BMC Genomics 4(13 Suppl):S3.
    • (2012) BMC Genomics , vol.4 , Issue.13 , pp. 3
    • Izarzugaza, J.M.G.1    Pozo, A.D.2    Vazquez, M.3    Valencia, A.4
  • 26
    • 84880832438 scopus 로고    scopus 로고
    • Prediction of disease causing non-synonymous SNPs by the artificial neural network predictor NetDiseaseSNP
    • Johansen, M. B., Izarzugaza, J. M. G., Brunak, S., Petersen, T. N., Gupta, R. (2013). Prediction of disease causing non-synonymous SNPs by the artificial neural network predictor NetDiseaseSNP. PLoS One 8:e68370.
    • (2013) PLoS One , vol.8
    • Johansen, M.B.1    Izarzugaza, J.M.G.2    Brunak, S.3    Petersen, T.N.4    Gupta, R.5
  • 30
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher, M, Witten, D, Jain, P, O'Roak, BJ, Cooper, GM, Shendure, J. 2014. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46:310–315.
    • (2014) Nat Genet , vol.46 , pp. 310-315
    • Kircher, M.1    Witten, D.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 31
    • 78049444976 scopus 로고    scopus 로고
    • Correlated mutations: a hallmark of phenotypic amino acid substitutions
    • Kowarsch, A., Fuchs, A., Frishman, D., Pagel, P. (2010). Correlated mutations: a hallmark of phenotypic amino acid substitutions. PLoS Comput Biol 6:e1000923.
    • (2010) PLoS Comput Biol , vol.6
    • Kowarsch, A.1    Fuchs, A.2    Frishman, D.3    Pagel, P.4
  • 32
    • 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, P. C. (2009). Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4:1073–1081.
    • (2009) Nat Protoc , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 33
    • 84929461414 scopus 로고    scopus 로고
    • Assessment of the predictive accuracy of five in silico prediction tools, alone or in combination, and two metaservers to classify long QT syndrome gene mutations
    • Leong, I. U. S., Stuckey, A., Lai, D., Skinner, J. R., Love, D. R. (2015). Assessment of the predictive accuracy of five in silico prediction tools, alone or in combination, and two metaservers to classify long QT syndrome gene mutations. BMC Med Genet 16:34.
    • (2015) BMC Med Genet , vol.16 , pp. 34
    • Leong, I.U.S.1    Stuckey, A.2    Lai, D.3    Skinner, J.R.4    Love, D.R.5
  • 34
    • 84937582018 scopus 로고    scopus 로고
    • Gene-specific function prediction for non-synonymous mutations in monogenic diabetes genes
    • Li, Q., Liu, X., Gibbs, R., Boerwinkle, E., Polychronakos, C., Qu, H-Q. (2014). Gene-specific function prediction for non-synonymous mutations in monogenic diabetes genes. PLoS One 9:e104452.
    • (2014) PLoS One , vol.9
    • Li, Q.1    Liu, X.2    Gibbs, R.3    Boerwinkle, E.4    Polychronakos, C.5    Qu, H.-Q.6
  • 38
    • 84863857768 scopus 로고    scopus 로고
    • Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis
    • Masica, D. L., Sosnay, P. R., Cutting, G. R., Karchin, R. (2015). Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Hum Mutat 33:1276–1274.
    • (2015) Hum Mutat , vol.33 , pp. 1274-1276
    • Masica, D.L.1    Sosnay, P.R.2    Cutting, G.R.3    Karchin, R.4
  • 39
    • 0035026704 scopus 로고    scopus 로고
    • Predicting Deleterious amino acid substitutions
    • Ng, P. C., Henikoff, S. (2001). Predicting Deleterious amino acid substitutions. Genome Res 11:863–874.
    • (2001) Genome Res , vol.11 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 40
    • 84922351308 scopus 로고    scopus 로고
    • PON-P2: prediction method for fast and reliable identification of harmful variants
    • Niroula, A., Urolagin, S., Vihinen, M. (2015). PON-P2: prediction method for fast and reliable identification of harmful variants. PLoS One 10:e0117380.
    • (2015) PLoS One , vol.10
    • Niroula, A.1    Urolagin, S.2    Vihinen, M.3
  • 41
    • 84947023989 scopus 로고    scopus 로고
    • Classification of amino acid substitutions in mismatch repair proteins using PON-MMR2
    • Niroula, A., Vihinen, M. (2015). Classification of amino acid substitutions in mismatch repair proteins using PON-MMR2. Hum Mutat 36:1128–1134.
    • (2015) Hum Mutat , vol.36 , pp. 1128-1134
    • Niroula, A.1    Vihinen, M.2
  • 42
    • 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, W. W., Hegde, M., Lyon, E., Spector, E., Voelkerding, K., Rehm, H. L. (2015). 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 17:405–423.
    • (2015) Genet Med , vol.17 , pp. 405-423
    • 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
  • 44
    • 84898546367 scopus 로고    scopus 로고
    • Prediction of pathological mutations in proteins: the challenge of integrating sequence conservation and structure stability principles
    • Riera, C., Lois, S., de la Cruz, X. (2014). Prediction of pathological mutations in proteins: the challenge of integrating sequence conservation and structure stability principles. Wiley Interdiscip Rev Comput Mol Sci 4:249–268.
    • (2014) Wiley Interdiscip Rev Comput Mol Sci , vol.4 , pp. 249-268
    • Riera, C.1    Lois, S.2    de la Cruz, X.3
  • 46
    • 45949108954 scopus 로고    scopus 로고
    • Protein interactions in human genetic diseases
    • Schuster-Böckler, B., Bateman, A. (2008). Protein interactions in human genetic diseases. Genome Biol 9:R9.
    • (2008) Genome Biol , vol.9 , pp. 9
    • Schuster-Böckler, B.1    Bateman, A.2
  • 47
    • 84897456458 scopus 로고    scopus 로고
    • MutationTaster2: mutation prediction for the deep-sequencing age
    • Schwarz, J. M., Cooper, D. N., 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
  • 48
    • 79961190441 scopus 로고    scopus 로고
    • KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels
    • Stead, L. F., Wood, I. C., Westhead, D. R. (2011). KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels. Bioinformatics 27:2181–2186.
    • (2011) Bioinformatics , vol.27 , pp. 2181-2186
    • Stead, L.F.1    Wood, I.C.2    Westhead, D.R.3
  • 49
    • 84867113601 scopus 로고    scopus 로고
    • Inferring causality and functional significance of human coding DNA variants
    • Sunyaev, S. R. (2012). Inferring causality and functional significance of human coding DNA variants. Hum Mol Genet 21:10–17.
    • (2012) Hum Mol Genet , vol.21 , pp. 10-17
    • Sunyaev, S.R.1
  • 50
    • 84925267288 scopus 로고    scopus 로고
    • UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
    • Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H. (2015). UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31:926–932.
    • (2015) Bioinformatics , vol.31 , pp. 926-932
    • Suzek, B.E.1    Wang, Y.2    Huang, H.3    McGarvey, P.B.4    Wu, C.H.5
  • 51
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: a hub for protein information
    • The UniProt Consortium. (2014). UniProt: a hub for protein information. Nucleic Acids Res 43:D204–D212.
    • (2014) Nucleic Acids Res , vol.43 , pp. D204-D212
  • 52
    • 65649108490 scopus 로고    scopus 로고
    • Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods
    • Thusberg, J, Vihinen, M. 2009. Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Hum Mutat 30:703–714.
    • (2009) Hum Mutat , vol.30 , pp. 703-714
    • Thusberg, J.1    Vihinen, M.2
  • 53
    • 36448935249 scopus 로고    scopus 로고
    • Accurate prediction of deleterious protein kinase polymorphisms
    • Torkamani, A., Schork, N. J. (2007). Accurate prediction of deleterious protein kinase polymorphisms. Bioinformatics 23:2918–2925.
    • (2007) Bioinformatics , vol.23 , pp. 2918-2925
    • Torkamani, A.1    Schork, N.J.2
  • 54
    • 84873087051 scopus 로고    scopus 로고
    • Guidelines for reporting and using prediction tools for genetic variation analysis
    • Vihinen, M. (2013). Guidelines for reporting and using prediction tools for genetic variation analysis. Hum Mutat 34:275–282.
    • (2013) Hum Mutat , vol.34 , pp. 275-282
    • Vihinen, M.1
  • 55
    • 84904410108 scopus 로고    scopus 로고
    • Majority vote and other problems when using computational tools
    • Vihinen, M. (2014). Majority vote and other problems when using computational tools. Hum Mutat 35:912–914.
    • (2014) Hum Mutat , vol.35 , pp. 912-914
    • Vihinen, M.1
  • 56
    • 84938288116 scopus 로고    scopus 로고
    • Muddled genetic terms miss and mess the message
    • Vihinen, M. (2015). Muddled genetic terms miss and mess the message. Trends Genet 31:423–425.
    • (2015) Trends Genet , vol.31 , pp. 423-425
    • Vihinen, M.1
  • 57
    • 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 Res 38:e164.
    • (2010) Nucleic Acids Res , vol.38
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 58
    • 84879987629 scopus 로고    scopus 로고
    • The role of balanced training and testing data sets for binary classifiers in bioinformatics
    • Wei Q, Dunbrack RL. 2013. The role of balanced training and testing data sets for binary classifiers in bioinformatics. PLoS One 8:e67863.
    • (2013) PLoS One , vol.8
    • Wei, Q.1    Dunbrack, R.L.2
  • 59
    • 84930351608 scopus 로고    scopus 로고
    • Solving the molecular diagnostic testing conundrum for Mendelian disorders in the era of next-generation sequencing: single-gene, gene panel, or exome/genome sequencing
    • Xue Y, Ankala A, Wilcox WR, Hegde M. 2015. Solving the molecular diagnostic testing conundrum for Mendelian disorders in the era of next-generation sequencing: single-gene, gene panel, or exome/genome sequencing. Genet Med 17:444–451.
    • (2015) Genet Med , vol.17 , pp. 444-451
    • Xue, Y.1    Ankala, A.2    Wilcox, W.R.3    Hegde, M.4
  • 60
    • 40549095676 scopus 로고    scopus 로고
    • Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase
    • Yip, Y. L., Famiglietti, L. M., Gos, A., Duek, P. D., David, F. P., Gateau, A., Bairoch, A. (2008). Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Hum Mutat 29:361–366.
    • (2008) Hum Mutat , vol.29 , pp. 361-366
    • Yip, Y.L.1    Famiglietti, L.M.2    Gos, A.3    Duek, P.D.4    David, F.P.5    Gateau, A.6    Bairoch, A.7
  • 61
    • 25144523127 scopus 로고    scopus 로고
    • Loss of protein structure stability as a major causative factor in monogenic disease
    • Yue, P, Li, ZL, Moult, J. 2005. Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol 353:459–473.
    • (2005) J Mol Biol , vol.353 , pp. 459-473
    • Yue, P.1    Li, Z.L.2    Moult, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.