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Comprehensive Analysis of rsSNPs Associated with Hypertension Using In-Silico Bioinformatics Tools

DOI: 10.4236/oalib.1102839, PP. 1-24

Subject Areas: Bioinformatics

Keywords: Hypertension, SNPs, In-Silico

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Abstract

Genetic epidemiological studies have suggested that several genetic variants increase the risk for hypertension. It is likely that a number of genes rather than a single gene account for the heritability of this complex disorder. However, the genetic analysis of hypertension produced complex, inconsistent and nonreproducible results, which makes it difficult to draw conclusions about the association between specific genes and hypertension. Material and methods: In this study, we aimed to analyze SNPs that had been investigated in hypertension. These SNPs were collected from text-mind hypertension, obesity and diabetic (T-HOD) data base program, during the period of 31 may 2016. SNPs lists which were reported with hypertension were collected in excel file sheet and processed for analysis using different types of bioinformatics tools and programs. Results: SNPs were evaluated for their deleterious effect on the protein function and stability, in the present study, 7 SNPs were predicted deleterious (A288S, M731T, R172C, R50Q, G460W, K197N, G75V). Mutation3D server showed 3 of mutations (STEA4, PLD2, AZIN2, rs28933400, rs2286672, rs16835244 genes and corresponding rsSNPs respectively) were found to increase risk to hypertension.

Cite this paper

Gassoum, A. , Abdelraheem, N. E. and Elsadig, N. (2016). Comprehensive Analysis of rsSNPs Associated with Hypertension Using In-Silico Bioinformatics Tools. Open Access Library Journal, 3, e2839. doi: http://dx.doi.org/10.4236/oalib.1102839.

References

[1]  Lifton, R.P. (1996) Molecular Genetics of Human Blood Pressure Variation. Science, 272, 676-680.
http://dx.doi.org/10.1126/science.272.5262.676
[2]  Izawa, H., Yamada, Y., Okada, T., Tanaka, M., Hirayama, H. and Yokota, M. (2003) Prediction of Genetic Risk for Hypertension. Hypertension, 41, 1035-1040.
http://dx.doi.org/10.1161/01.HYP.0000065618.56368.24
[3]  Williams, S.M., et al. (2000) Combinations of Variations in Multiple Genes Are Associated with Hypertension. Hypertension, 36, 2-6.
http://dx.doi.org/10.1161/01.HYP.36.1.2
[4]  Dai, H.-J., Chang, Y.-C., Tsai, R.T.-H. and Hsu, W.-L. (2011) Integration of Gene Normalization Stages and Co-Reference Resolution Using a Markov Logic Network. Bioinformatics, 27, 2586-2594.
http://dx.doi.org/10.1093/bioinformatics/btr358
[5]  Dai, H.-J., Lai, P.-T. and Tsai, R.T.-H. (2010) Multistage Gene Normalization and SVM-Based Ranking for Protein Interactor Extraction in Full-Text Articles. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7, 412-420.
[6]  Tsai, R.T.-H., Lai, P.-T., Dai, H.-J., et al. (2009) HypertenGene: Extracting Key Hypertension Genes from Biomedical Literature with Position and Automatically-Generated Template Features. BMC Bioinformatics, 10, S9.
http://dx.doi.org/10.1186/1471-2105-10-S15-S9
[7]  Single Nucleotide Polymorphism/SNP (2015) Learn Science at Scitable.
http://www.nature.com  
[8]  Nachman, M.W. (2001) Single Nucleotide Polymorphisms and Recombination Rate in Humans. Trends in Genetics, 17, 481-485.
http://dx.doi.org/10.1016/S0168-9525(01)02409-X
[9]  Varela, M.A. and Amos, W. (2010) Heterogeneous Distribution of SNPs in the Human Genome: Microsatellites as Predictors of Nucleotide Diversity and Divergence. Genomics, 95, 151-159.
http://dx.doi.org/10.1016/j.ygeno.2009.12.003
[10]  Barreiro, L.B., Laval, G., Quach, H., Patin, E. and Quintana-Murci, L. (2008) Natural Selection has Driven Population Differentiation in Modern Humans. Nature Genetics, 40, 340-345.
http://dx.doi.org/10.1038/ng.78

[11]  Hodgkinson, A. and Eyre-Walker, A. (2009) Human Triallelic Sites: Evidence for a New Mutational Mechanism? Genetics, 1.
[12]  Ingram, V.M. (1956) A Specific Chemical Difference between the Globins of Normal Human and Sickle-Cell Anaemia Haemoglobin. Nature, 178, 792-794.
http://dx.doi.org/10.1038/178792a0
[13]  Chang, J.C. and Kan, Y.W. (1979) Beta 0 Thalassemia, a Nonsense Mutation in Man. Proceedings of the National Academy of Sciences of the United States of America, 76, 2886-2889.
http://dx.doi.org/10.1073/pnas.76.6.2886
[14]  Hamosh, A., King, T.M., Rosenstein, B.J., Corey, M., Levison, H., Durie, P., Tsui, L.C., McIntosh, I., Keston, M., Brock, D.J., Macek, M., Zemková, D., Krásni?anová, H., Vávrová, V., Macek, M., Golder, N., Schwarz, M.J., Super, M., Watson, E.K., Williams, C., Bush, A., O’Mahoney, S.M., Humphries, P., Dearce, M.A., Reis, A., Bürger, J., Stuhrmann, M., Schmidtke, J., Wulbrand, U. and D?rk, T. (1992) Cystic Fibrosis Patients Bearing Both the Common Missense Mutation Gly-Asp at Codon 551 and the Delta F508 Mutation Are Clinically Indistinguishable from Delta F508 Homozygotes, Except for Decreased Risk of Meconiumileus. American Journal of Human Genetics, 51, 245- 250.
[15]  Wolf, A.B., Caselli, R.J., Reiman, E.M. and Valla, J. (2012) APOE and Neuroenergetics: An Emerging Paradigm in Alzheimer’s Disease. Neurobiology of Aging, 34, 1007-1017.
http://dx.doi.org/10.1016/j.neurobiolaging.2012.10.011
[16]  Abecasis, G.R. and Cookson, W.O. (2000) GOLD—Graphical Overview of Linkage Disequilibrium. Bioinformatics, 16, 182-183.
http://dx.doi.org/10.1093/bioinformatics/16.2.182
[17]  Thomas, P.E., Klinger, R., Furlong, L.I., Hofmann-Apitius, M. and Friedrich, C.M. (2011) Challenges in the Association of Human Single Nucleotide Polymorphism Mentions with Unique Database Identifiers. BMC Bioinformatics, 12, S4.
http://dx.doi.org/10.1186/1471-2105-12-S4-S4
[18]  Singh, M., Singh, P., Juneja, P.K., Singh, S. and Kaur, T. (2010) SNP-SNP Interactions within APOE Gene Influence Plasma Lipids in Postmenopausal Osteoporosis. Rheumatology International, 31, 421-423.
http://dx.doi.org/10.1007/s00296-010-1449-7
[19]  Li, G., Pan, T., Guo, D. and Li, L.C. (2014) Regulatory Variants and Disease: The E-Cadherin-160C/A SNP as an Example. Molecular Biology International, 2014, Article ID: 967565.
http://dx.doi.org/10.1155/2014/967565
[20]  Lu, Y.-F., Mauger, D.M., Goldstein, D.B., Urban, T.J., Weeks, K.M. and Bradrick, S.S. (2015) IFNL3 mRNA Structure Is Remodeled by a Functional Non-Coding Polymorphism Associated with Hepatitis C Virus Clearance. Scientific Reports, 5, Article No. 16037.
http://dx.doi.org/10.1038/srep16037
[21]  Kimchi-Sarfaty, C., Oh, J.M., Kim, I.W., Sauna, Z.E., Calcagno, A.M., Ambudkar, S.V. and Gottesman, M.M. (2007) A “Silent” Polymorphism in the MDR1 Gene Changes Substrate Specificity. Science, 315, 525-528.
http://dx.doi.org/10.1126/science.1135308
[22]  Al-Haggar, M., Madej-Pilarczyk, A., Kozlowski, L., Bujnicki, J.M., Yahia, S., Abdel-Hadi, D., Shams, A., Ahmad, N., Hamed, S. and Puzianowska-Kuznicka, M. (2012) A Novel Homozygous p.Arg527Leu LMNA Mutation in Two Unrelated Egyptian Families Causes Overlapping Mandibuloacral Dysplasia and Progeria Syndrome. European Journal of Human Genetics, 20, 1134-1140.
http://dx.doi.org/10.1038/ejhg.2012.77
[23]  Cordovado, S.K., Hendrix, M., Greene, C.N., Mochal, S., Earley, M.C., Farrell, P.M., Kharrazi, M., Hannon, W.H. and Mueller, P.W. (2012) CFTR Mutation Analysis and Haplotype Associations in CF Patients. Molecular Genetics and Metabolism, 105, 249-254.
[24]  Talavera, D., Robertson, D.L. and Lovell, S.C. (2011) Characterization of Protein-Protein Interaction Interfaces from a Single Species. PLoS ONE, 6, e21053.
http://dx.doi.org/10.1371/journal.pone.0021053
[25]  Andreani, J., Faure, G. and Guerois, R. (2012) Versatility and in Variance in the Evolution of Homologous Heteromeric Interfaces. PLoS Computational Biology, 8, e1002677.
http://dx.doi.org/10.1371/journal.pcbi.1002677
[26]  Calabrese, R., Capriotti, E., Fariselli, P., Martelli, P.L. and Casadio, R. (2009) Functional Annotations Improve the Predictive Score of Human Disease-Related Mutations in Proteins. Human Mutation, 30, 1237-1244.
http://dx.doi.org/10.1002/humu.21047
[27]  Capriotti, E., Fariselli, P. and Casadio, R. (2005) I-Mutant2.0: Predicting Stability Changes upon Mutation from the Protein Sequence or Structure. Nucleic Acids Research, 33, 306-310.
http://dx.doi.org/10.1093/nar/gki375

[28]  Sofia, B.M. and Mohamed, M.H. (2016) Insilico Validation of Babesia Bovis Merozoite Surface Antigen-1, Merozoite Surface Antigen-2b and Merozoite Surface Antigen-2c Proteins for Vaccine and Drug Development. International Journal of Bioinformatics and Biomedical Engineering, 2, 30-39.
[29]  Guharoy, M. and Chakrabarti, P. (2005) Conservation and Relative Importance of Residues across Protein-Protein Interfaces. Proceedings of the National Academy of Sciences of the United States of America, 102, 15447-15452.
[30]  Venselaar, H., te Beek, T.A.H., Kuipers, R.K.P., Hekkelman, M.L. and Vriend, G. (2010) Protein Structure Analysis of Mutations Causing Inheritable Diseases. An e-Science Approach with Life Scientist Friendly Interfaces. BMC Bioinformatics, 11, 548.
http://dx.doi.org/10.1186/1471-2105-11-548
[31]  K?llberg, M., Wang, H.P., Wang, S., Peng, J., Wang, Z.Y., Lu, H. and Xu, J.B. (2012) Template-Based Protein Structure Modeling Using the RaptorX Web Server. Nature Protocols, 7, 1511-1522.
http://dx.doi.org/10.1038/nprot.2012.085
[32]  Ma, J.Z., Wang, S., Zhao, F. and Xu, J.B. (2013) Protein Threading Using Context-Specific Alignment Potential. Bioinformatics, 29, i257-i265.
http://dx.doi.org/10.1093/bioinformatics/btt210
[33]  Peng, J. and Xu, J.B. (2011) A Multiple-Template Approach to Protein Threading. Proteins, 79, 1930-1939.
http://dx.doi.org/10.1002/prot.23016
[34]  Peng, J. and Xu, J.B. (2011) RaptorX: Exploiting Structure Information for Protein Alignment by Statistical Inference. Proteins, 79, 161-171.
http://dx.doi.org/10.1002/prot.23175
[35]  Kumar, P., Henikoff, S. and Ng, P.C. (2009) Predicting the Effects of Coding Non-Synonymous Variants on Protein Function Using the SIFT Algorithm. Nature Protocols, 4, 1073-1081.
http://dx.doi.org/10.1038/nprot.2009.86
[36]  Choi, Y., Sims, G.E., Murphy, S., Miller, J.R. and Chan, A.P. (2012) Predicting the Functional Effect of Amino Acid Substitutions and Indels. PLoS ONE, 7, e46688.
http://dx.doi.org/10.1371/journal.pone.0046688

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