BALL-SNP: Combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms

Genome Medicine

Volumn 7, Issue 1, 2015, Pages

  Mueller, Sabine C ^a   Backes, Christina ^a   Kalinina, Olga V ^d   Meder, Benjamin ^b,c   Stöckel, Daniel ^a   Lenhof, Hans Peter ^a   Meese, Eckart ^a   Keller, Andreas ^a  

^a SAARLAND UNIVERSITY   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c DZHK GERMAN CENTRE FOR CARDIOVASCULAR RESEARCH   (Germany)

^d MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; AUTOMATION; BALL SNP ALGORITHM; BINDING SITE; CARDIOMYOPATHY; GENE; GENE CLUSTER; GENE MUTATION; GENETIC ALGORITHM; GENETIC SELECTION; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; JUP GENE; PATHOGENICITY; PREDICTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN BINDING; PROTEIN DATA BANK; PROTEIN STABILITY; PROTEIN STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; SMYD2 GENE; VCL GENE;

EID: 84937213579     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0190-y     Document Type: Article

References (28)

1. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A. 2009;106:19096-101.
2. Thusberg J, Olatubosun A, Vihinen M. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat. 2011;32:358-68.
3. Castellana S, Mazza T. Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. Brief Bioinform. 2013;14:448-59.
4. Li M, Petukh M, Alexov E, Panchenko AR. Predicting the impact of missense mutations on protein-protein binding affinity. J Chem Theory Comput. 2014;10:1770-80.
5. Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol. 2002;320:369-87.
6. Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E. Molecular mechanisms of disease-causing missense mutations. J Mol Biol. 2013;425:3919-36.
7. Mueller SC, Backes C, Haas J. The Inheritance Study Group. Meder B, et al. Pathogenicity prediction of non-synonymous single nucleotide variants in dilated cardiomyopathy. Brief Bioinform: Katus HA; 2015. doi: 10.1093/bib/bbu054) 6.
8. Backes C, Harz C, Fischer U, Schmitt J, Ludwig N, Petersen BS, et al. New insights into the genetics of glioblastoma multiforme by familial exome sequencing. Oncotarget. 2015;6:5918-31.
9. Kucukkal TG, Petukh M, Li L, Alexov E. Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins. Curr Opin Struct Biol. 2015;32C:18-24.
10. Schork NJ, Murray SS, Frazer KA, Topol EJ. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev. 2009;19:212-9.
11. Wang Z, Moult J. SNPs, protein structure, and disease. Hum Mutat. 2001;17:263-70.
12. Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, et al. BALL--biochemical algorithms library 1.3. BMC Bioinformatics. 2010;11:531.
13. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42:D980-5.
14. Wu CH, Apweiler R, Bairoch A, Natale DA, Broeckmann B, Ferro S, et al. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 2006;34:D187-91.
15. Haas J, Frese KS, Peil B, Kloos W, Keller A, Nietsch R, et al. Atlas of the clinical genetics of human dilated cardiomyopathy. Eur Heart J. 2015;36:1123-35.
16. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308-11.
17. Yip YL, Famiglietti M, Gos A, Duek PD, David FP, Gateau A, et al. Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Hum Mutat. 2008;29:361-6.
18. Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN, et al. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet. 2014;133:1-9.
19. Moll A, Hildebrandt A, Lenhof HP, Kohlbacher O. BALLView: a tool for research and education in molecular modeling. Bioinformatics. 2006;22:365-6.
20. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38, e164.
21. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Res. 2000;28:235-42.
22. Traina C, Traina A, Wu L, Faloutsos C. Fast feature selection using fractal dimensions. In: Proceedings of the 15th Brazilian Symposium on Databases. Pittsburgh, PA: Carnegie Mellon University, 2000. Available at: http://repository.cmu.edu/cgi/viewcontent.cgi?article=1572&context=compsci
23. Dehouck Y, Kwasigroch JM, Rooman M, Gilis D. BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations. Nucleic Acids Res. 2013;41:W333-9.
24. Capriotti E, Fariselli P, Casadio R. A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics. 2004;20:i63-8.
25. Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 2005;33:W306-10.
26. BALL-SNP homepage. Available at: http://www.ccb.uni-saarland.de/BALL-SNP.
27. Asimaki A, Syrris P, Wichter T, Matthias P, Saffitz JE, McKenna WJ. A novel dominant mutation in plakoglobin causes arrhythmogenic right ventricular cardiomyopathy. Am J Hum Genet. 2007;81:964-73.
28. Olson TM, Illenberger S, Kishimoto NY, Huttelmaier S, Keating MT, Jockusch BM. Metavinculin mutations alter actin interaction in dilated cardiomyopathy. Circulation. 2002;105:431-7.