Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed.
作者： Stephanie Hicks , David A. Wheeler , Sharon E. Plon , Marek Kimmel
DOI: 10.1002/HUMU.21490
关键词:
摘要: Multiple algorithms are used to predict the impact of missense mutations on protein structure and function using algorithm-generated sequence alignments or manually curated alignments. We compared accuracy with native alignment SIFT, Align-GVGD, PolyPhen-2, Xvar when generating functionality predictions well-characterized (n = 267) within BRCA1, MSH2, MLH1, TP53 genes. also evaluated employed from these (except Xvar) supplied same four including automatically generated by (1) (2) Polyphen-2, (3) Uniprot, (4) a tuned for Align-GVGD. Alignments differ in composition evolutionary depth. Data-based receiver operating characteristic curves employing each algorithm result area under curve 78-79% all algorithms. Predictions PolyPhen-2 were least dependent employed. In contrast, Align-GVGD predicts variants neutral provided large number sequences. Of note, make different even do not necessarily perform best their own alignment. Thus, researchers should consider optimizing both prediction.
elsevier.com
sci-hub.se 参考文章(30)
Rachel Karchin, Mukesh Agarwal, Andrej Sali, Fergus Couch, Mary S. Beattie, Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. Cancer Informatics. ,vol. 6, pp. 203- 216 ,(2008) , 10.4137/CIN.S618
M S Greenblatt, J G Beaudet, J R Gump, K S Godin, L Trombley, J Koh, J P Bond, Detailed computational study of p53 and p16: using evolutionary sequence analysis and disease-associated mutations to predict the functional consequences of allelic variants. Oncogene. ,vol. 22, pp. 1150- 1163 ,(2003) , 10.1038/SJ.ONC.1206101
Sean V. Tavtigian, Marc S. Greenblatt, Fabienne Lesueur, Graham B. Byrnes, , In silico analysis of missense substitutions using sequence-alignment based methods. Human Mutation. ,vol. 29, pp. 1327- 1336 ,(2008) , 10.1002/HUMU.20892
David E. Goldgar, Douglas F. Easton, Amie M. Deffenbaugh, Alvaro N.A. Monteiro, Sean V. Tavtigian, Fergus J. Couch, Integrated Evaluation of DNA Sequence Variants of Unknown Clinical Significance: Application to BRCA1 and BRCA2 The American Journal of Human Genetics. ,vol. 75, pp. 535- 544 ,(2004) , 10.1086/424388
Daniel M Jordan, Vasily E Ramensky, Shamil R Sunyaev, Human allelic variation: perspective from protein function, structure, and evolution Current Opinion in Structural Biology. ,vol. 20, pp. 342- 350 ,(2010) , 10.1016/J.SBI.2010.03.006
Csilla Szabo, Anthony Masiello, Joseph F. Ryan, Lawrence C. Brody, , The breast cancer information core: database design, structure, and scope. Human Mutation. ,vol. 16, pp. 123- 131 ,(2000) , 10.1002/1098-1004(200008)16:2<123::AID-HUMU4>3.0.CO;2-Y
Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev, A method and server for predicting damaging missense mutations Nature Methods. ,vol. 7, pp. 248- 249 ,(2010) , 10.1038/NMETH0410-248
Janita Thusberg, Mauno Vihinen, Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Human Mutation. ,vol. 30, pp. 703- 714 ,(2009) , 10.1002/HUMU.20938
Magali Olivier, Ros Eeles, Monica Hollstein, Mohammed A. Khan, Curtis C. Harris, Pierre Hainaut, The IARC TP53 database: new online mutation analysis and recommendations to users. Human Mutation. ,vol. 19, pp. 607- 614 ,(2002) , 10.1002/HUMU.10081
Thomas D. Schneider, Gary D. Stormo, Larry Gold, Andrzej Ehrenfeucht, Information content of binding sites on nucleotide sequences Journal of Molecular Biology. ,vol. 188, pp. 415- 431 ,(1986) , 10.1016/0022-2836(86)90165-8