Table of Contents Author Guidelines Submit a Manuscript
Advances in Bioinformatics
Volume 2016, Article ID 2632917, 15 pages
http://dx.doi.org/10.1155/2016/2632917
Research Article

Bioinformatics Approach for Prediction of Functional Coding/Noncoding Simple Polymorphisms (SNPs/Indels) in Human BRAF Gene

1Faculty of Medical Laboratory Sciences, University of Medical Science and Technology, Khartoum, Sudan
2Department of Biotechnology, Faculty of Applied and Industrial Science, University of Juba, Khartoum, Sudan
3Faculty of Pharmacy, Omdurman Islamic University, Khartoum, Sudan
4Faculty of Science, University of Khartoum, Khartoum, Sudan
5Faculty of Medical Laboratory Sciences, Karary University, Khartoum, Sudan
6Tropical Medicine Research Institute, Khartoum, Sudan

Received 26 November 2015; Revised 10 May 2016; Accepted 12 May 2016

Academic Editor: Ming Chen

Copyright © 2016 Mohamed M. Hassan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. Volante, P. Collini, Y. E. Nikiforov et al., “Poorly differentiated thyroid carcinoma: the Turin proposal for the use of uniform diagnostic criteria and an algorithmic diagnostic approach,” American Journal of Surgical Pathology, vol. 31, no. 8, pp. 1256–1264, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. R. H. Grogan, E. J. Mitmaker, and O. H. Clark, “The evolution of biomarkers in thyroid cancer-from mass screening to a personalized biosignature,” Cancers, vol. 2, no. 2, pp. 885–912, 2010. View at Publisher · View at Google Scholar · View at Scopus
  3. E. Domingo and S. Schwartz Jr., “BRAF (v-raf murine sarcoma viral oncogene homolog B1),” Atlas of Genetics and Cytogenetics in Oncology and Haematology, vol. 8, no. 4, pp. 302–306, 2004. View at Publisher · View at Google Scholar
  4. M. R. M. Hussain, M. Baig, H. S. A. Mohamoud et al., “BRAF gene: from human cancers to developmental syndromes,” Saudi Journal of Biological Sciences, vol. 22, no. 4, pp. 359–373, 2015. View at Publisher · View at Google Scholar
  5. R. D. Hall and R. R. Kudchadkar, “Braf mutations: signaling, epidemiology, and clinical experience in multiple malignancies,” Cancer Control, vol. 21, no. 3, pp. 221–230, 2014. View at Google Scholar · View at Scopus
  6. M. R. M. Hussain, M. Baig, H. S. A. Mohamoud et al., “BRAF gene: from human cancers to developmental syndromes,” Saudi Journal of Biological Sciences, vol. 22, no. 4, pp. 359–373, 2015. View at Publisher · View at Google Scholar
  7. J. Bosco, A. Allende, W. Varikatt, R. Lee, and G. J. Stewart, “Does the BRAFV600E mutation herald a new treatment era for Erdheim-Chester disease? A case-based review of a rare and difficult to diagnose disorder,” Internal Medicine Journal, vol. 45, no. 3, pp. 348–351, 2015. View at Publisher · View at Google Scholar · View at Scopus
  8. R. Guerra and Z. Yu, “Single nucleotide polymorphisms and their applications,” in Computational and Statistical Approaches to Genomics, W. Zhang and I. Shmulevich, Eds., chapter 16, pp. 311–349, Springer, Berlin, Germany, 2006. View at Publisher · View at Google Scholar
  9. M. M. Hassan, A. A. Dowd, A. H. Mohamed et al., “Computational analysis of deleterious nsSNPs within HLA-DRB1 and HLA-DQB1 genes responsible for Allograft rejection,” International Journal of Computational Bioinformatics and in Silico Modeling, vol. 3, no. 6, pp. 562–577, 2014. View at Google Scholar
  10. M. Alanazi, Z. Abduljaleel, W. Khan et al., “In silico analysis of single nucleotide polymorphism (SNPs) in human β-globin gene,” PLoS ONE, vol. 6, no. 10, Article ID e25876, 2011. View at Google Scholar
  11. A. A. Komar and Humana Press, Single Nucleotide Polymorphism-Methods and Protocols, vol. 578, Humana Press, Totowa, NJ, USA, 2009.
  12. E. M. Smigielski, K. Sirotkin, M. Ward, and S. T. Sherry, “dbSNP: a database of single nucleotide polymorphisms,” Nucleic Acids Research, vol. 28, no. 1, pp. 352–355, 2000. View at Publisher · View at Google Scholar · View at Scopus
  13. A. Bhattacharya, J. D. Ziebarth, and Y. Cui, “PolymiRTS Database 3.0: Linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways,” Nucleic Acids Research, vol. 42, no. 1, pp. D86–D91, 2014. View at Publisher · View at Google Scholar · View at Scopus
  14. P. Kumar, J. Hu, S. Henikoff, G. Schneider, C. Pauline, and P. C. Ng, “SIFT web server: predicting effects of amino acid substitutions on proteins,” Nucleic Acids Research, vol. 40, no. 1, pp. W452–W457, 2012. View at Publisher · View at Google Scholar
  15. P. Kumar, S. Henikoff, and P. C. Ng, “Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm,” Nature Protocols, vol. 4, no. 7, pp. 1073–1082, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. S. M. O. Sarour, A. M. Zayed, M. O. M. Ibrahim et al., “New mutation found within OTOR gene involved in deafness in two Sudanese families from Al-Jazirah state-Sudan: using Next Generation Sequencing (NGS),” Bio-Genetics Journal, vol. 2, no. 6, pp. 46–50, 2014. View at Google Scholar
  17. M. Hecht, Y. Bromberg, and B. Rost, “News from the protein mutability landscape,” Journal of Molecular Biology, vol. 425, no. 21, pp. 3937–3948, 2013. View at Publisher · View at Google Scholar
  18. E. Capriotti, P. Fariselli, R. Calabrese, and R. Casadio, “Predicting protein stability changes from sequences using support vector machines,” Bioinformatics, vol. 21, no. 2, pp. ii54–ii58, 2005. View at Publisher · View at Google Scholar · View at Scopus
  19. M. Nielsen, C. Lundegaard, O. Lund, and T. N. Petersen, “CPHmodels 3.2.remote homology modeling using structure-guided sequence profiles,” Nucleic Acids Research, vol. 38, pp. W576–W581, 2010, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896139/pdf/gkq535.pdf. View at Publisher · View at Google Scholar
  20. G. S. Couch, D. K. Hendrix, and T. E. Ferrin, “Nucleic acid visualization with UCSF Chimera,” Nucleic Acids Research, vol. 34, no. 4, article e29, pp. 1–5, 2006. View at Google Scholar
  21. H. Venselaar, T. A. H. te Beek, R. K. P. Kuipers, M. L. Hekkelman, and G. Vriend, “Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces,” BMC Bioinformatics, vol. 11, article 548, 2010. View at Publisher · View at Google Scholar · View at Scopus
  22. D. Farré, R. Roset, M. Huerta et al., “Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN,” Nucleic Acids Research, vol. 31, no. 13, pp. 3651–3653, 2003. View at Publisher · View at Google Scholar · View at Scopus
  23. F. Desmet, D. Hamroun, M. Lalande, G. Collod-Beroud, M. Claustres, and C. Beroud, “Human Splicing Finder: an online bioinformatics tool to predict splicing signals,” Nucleic Acids Research, vol. 37, no. 9, pp. e67–e67, 2009, http://nar.oxfordjournals.org/content/early/2009/04/01/nar.gkp215.full.pdf+html. View at Publisher · View at Google Scholar
  24. Y. H. Tan, Y. Liu, K. W. Eu et al., “Detection of BRAF V600E mutation by pyrosequencing,” Pathology, vol. 40, no. 3, pp. 295–298, 2008. View at Publisher · View at Google Scholar · View at Scopus
  25. M. Yarchoan, V. A. LiVolsi, and M. S. Brose, “BRAF mutation and thyroid cancer recurrence,” Journal of Clinical Oncology, vol. 33, no. 1, pp. 7–8, 2015, http://jco.ascopubs.org/content/early/2014/11/20/JCO.2014.59.3657.full.pdf+html. View at Publisher · View at Google Scholar