A gene-specific method for predicting hemophilia-causing point mutations

Nobuko Hamasaki-Katagiri, Raheleh Salari, Andrew Wu, Yini Qi, Tal Schiller, Amanda C. Filiberto, Enrique F. Schisterman, Anton A. Komar, Teresa M. Przytycka, Chava Kimchi-Sarfaty

Research output: Contribution to journalArticle

Abstract

A fundamental goal of medical genetics is the accurate prediction of genotype-phenotype correlations. As an approach to develop more accurate in silico tools for prediction of disease-causing mutations of structural proteins, we present a gene- and disease-specific prediction tool based on a large systematic analysis of missense mutations from hemophilia A (HA) patients. Our HA-specific prediction tool, HApredictor, showed disease prediction accuracy comparable to other publicly available prediction software. In contrast to those methods, its performance is not limited to non-synonymous mutations. Given the role of synonymous mutations in disease and drug codon optimization, we propose that utilizing a gene- and disease-specific method can be highly useful to make functional predictions possible even for synonymous mutations. Incorporating computational metrics at both nucleotide and amino acid levels along with multiple protein sequence/structure alignment significantly improved the predictive performance of our tool. HApredictor is freely available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/HA-Predict/index.htm.

Original languageEnglish (US)
Pages (from-to)4023-4033
Number of pages11
JournalJournal of Molecular Biology
Volume425
Issue number21
DOIs
StatePublished - Nov 1 2013
Externally publishedYes

Fingerprint

Hemophilia A
Point Mutation
Genes
Mutation
Sequence Alignment
Medical Genetics
Genetic Association Studies
Missense Mutation
Codon
Computer Simulation
Proteins
Software
Nucleotides
Amino Acids
Pharmaceutical Preparations
Silent Mutation

Keywords

  • coagulation factor IX
  • coagulation factor VIII
  • gene/disease-specific prediction tool
  • hemophilia A/B
  • synonymous mutation

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Hamasaki-Katagiri, N., Salari, R., Wu, A., Qi, Y., Schiller, T., Filiberto, A. C., ... Kimchi-Sarfaty, C. (2013). A gene-specific method for predicting hemophilia-causing point mutations. Journal of Molecular Biology, 425(21), 4023-4033. https://doi.org/10.1016/j.jmb.2013.07.037

A gene-specific method for predicting hemophilia-causing point mutations. / Hamasaki-Katagiri, Nobuko; Salari, Raheleh; Wu, Andrew; Qi, Yini; Schiller, Tal; Filiberto, Amanda C.; Schisterman, Enrique F.; Komar, Anton A.; Przytycka, Teresa M.; Kimchi-Sarfaty, Chava.

In: Journal of Molecular Biology, Vol. 425, No. 21, 01.11.2013, p. 4023-4033.

Research output: Contribution to journalArticle

Hamasaki-Katagiri, N, Salari, R, Wu, A, Qi, Y, Schiller, T, Filiberto, AC, Schisterman, EF, Komar, AA, Przytycka, TM & Kimchi-Sarfaty, C 2013, 'A gene-specific method for predicting hemophilia-causing point mutations', Journal of Molecular Biology, vol. 425, no. 21, pp. 4023-4033. https://doi.org/10.1016/j.jmb.2013.07.037
Hamasaki-Katagiri N, Salari R, Wu A, Qi Y, Schiller T, Filiberto AC et al. A gene-specific method for predicting hemophilia-causing point mutations. Journal of Molecular Biology. 2013 Nov 1;425(21):4023-4033. https://doi.org/10.1016/j.jmb.2013.07.037
Hamasaki-Katagiri, Nobuko ; Salari, Raheleh ; Wu, Andrew ; Qi, Yini ; Schiller, Tal ; Filiberto, Amanda C. ; Schisterman, Enrique F. ; Komar, Anton A. ; Przytycka, Teresa M. ; Kimchi-Sarfaty, Chava. / A gene-specific method for predicting hemophilia-causing point mutations. In: Journal of Molecular Biology. 2013 ; Vol. 425, No. 21. pp. 4023-4033.
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