IN SILICO STUDY OF DELETERIOUS SINGLE NUCLEOTIDE POLYMORPHISMS IN HUMAN HTRA2 GENE WITH THE PARKINSON’S DISEASE

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OMAR QAHTAN YASEEN

Abstract

One of the most prevalent neurodegenerative illnesses that affects the elderly and is incurable is Parkinson's disease. Effective remedies for these illnesses are sometimes expensive, time-consuming, and coincidental to find. Prior research comparing several model organisms has shown that the majority of animals have comparable cellular and molecular traits. The Bioinformatics tools were used to find non-synonymous single nucleotide polymorphisms SIFTand Mutpred. The HTRA2 protein, a protein linked to Parkinson's disease, was used to predict nsSNPs.


This study is based on the analysis of single nucleotide polymorphisms in the human HTRA2 gene that cause Parkinson's disease. By determining the most effective prediagnosis techniques and Biological markers for illness prediction.


Our goal is to identify the most effective prediagnosis method for Parkinson's disease. A specific SNP is to serve as a molecular marker for the illness's prediagnosis. The analysis of non-synonymous SNPs (nsSNPs) in several Bioinformatics methods may facilitate the identification of critical diagnoses for the disease and enhance the treatment process for Parkinson's disease (PD).

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References

Checkoway, H., Lundin, J. I. & Kelada, S. N. Neurodegenerative diseases. IARC Sci. Publ. 163, 407–419 (2011).

Ali, A. M. & Kunugi, H. Royal jelly as an intelligent anti-aging agent—A focus on cognitive aging and Alzheimer’s disease: A review. Antioxidants 9(10), 1–46. https://doi.org/10.3390/antiox9100937 (2020).

Chekani, F., Bali, V. & Aparasu, R. R. Quality of life of patients with Parkinson’s disease and neurodegenerative dementia: A nationally representative study. Res. Soc. Adm. Pharm. 12(4), 604–613. https://doi.org/10.1016/j.sapharm.2015.09.007 (2016).

Denell, R. Establishment of tribolium as a genetic model system and its early contributions to evo-devo. Genetics 180(4), 1779–1786. https://doi.org/10.1534/genetics.104.98673 (2008).

Bingsohn, L., Knorr, E. & Vilcinskas, A. Te model beetle Tribolium castaneum can be used as an early warning system for transgenerational epigenetic side efects caused by pharmaceuticals. Comp. Biochem. Physiol. Part C Toxicol. Pharmacol. 185, 57–64 (2016).

Jia, M. et al. Computational analysis of functional single nucleotide polymorphisms associated with the CYP11B2 gene. PLoS ONE 9(8), e104311 (2014).

Mooney, S. D., Krishnan, V. G. & Evani, U. S. Bioinformatic tools for identifying disease gene and SNP candidates. Methods Mol. Biol. 628, 307–319. https://doi.org/10.1007/978-1-60327-367-1_17 (2010).

Bromberg, Y. Chapter 15: Disease gene prioritization. In PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.10029 02 (2013).

Tey, H. J. & Ng, C. H. Computational analysis of functional SNPs in Alzheimer’s disease-associated endocytosis genes. PeerJ https:// doi.org/10.7717/peerj.7667 (2019).

Sim, N. L. et al. SIFT web server: Predicting efects of amino acid substitutions on proteins. Nucleic Acids Res. 40(W1), W452–W457 (2012).

Tomas, P. D. et al. PANTHER: A library of protein families and subfamilies indexed by function. Genome Res. 13(9), 2129–2141 (2003).

Bromberg, Y. & Rost, B. SNAP: Predict efect of non-synonymous polymorphisms on function. Nucleic Acids Res. 35(11), 3823–3835 (2007).

Capriotti, E. & Fariselli, P. PhD-SNPg: A webserver and lightweight tool for scoring single nucleotide variants. Nucleic Acids Res. 45(W1), W247–W252 (2017).

Tahseen, T. H. (2019). The impact of the educational method using the training method in some physical variables of the muscles of the limbs and the strength of the transmissions in the game of tennis. University of Anbar Sport and Physical Education Science Journal, 4(18).28. Hoeppner, M. A. NCBI Bookshelf: Books and documents in life sciences and health care. Nucleic Acids Res. 41(D1), D1251–D1260 (2012).

Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27–30. https://doi.org/10. 1093/nar/28.1.27 (2000).

Kanehisa, M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. Publ. Protein Soc. 28(11), 1947– 1951. https://doi.org/10.1002/pro.3715 (2019).

Qahtan, O. (2023). Sorting Intolerant from Tolerant and PolyPhen-2 Algorithms: A Variation in Exon 14 of ATP7B Gene among 4 West Iraqi Families with Wilson’s Disease. Al-Anbar Medical Journal, 19(2), 98-103.‏

Yaseen, O. Q., Al-Ani, M. Q., & Majeed, Y. H. (2020). In-Silico prediction of impact on protein function caused by non-synonymous single nucleotide polymorphism in human ATP7B gene associated with Wilson disease. Research Journal of Biotechnology Vol, 15, 3.‏

Constantinescu, A. E., Hughes, D. A., Bull, C. J., Fleming, K., Mitchell, R. E., Zheng, J., ... & Vincent, E. E. (2024). A genome-wide association study of neutrophil count in individuals associated to an African continental ancestry group facilitates studies of malaria pathogenesis. Human Genomics, 18(1), 26.‏

Aspatwar, A., Tolvanen, M. E., Barker, H., Syrjänen, L., Valanne, S., Purmonen, S., ... & Parkkila, S. (2022). Carbonic anhydrases in metazoan model organisms: molecules, mechanisms, and physiology. Physiological reviews, 102(3), 1327-1383.‏

Al-Ayari, E. A., Shehata, M. G., El-Hadidi, M., & Shaalan, M. G. (2023). In silico SNP prediction of selected protein orthologues in insect models for Alzheimer's, Parkinson's, and Huntington’s diseases. Scientific Reports, 13(1), 18986.‏

Hussein, A. F., Khamees, H. H., Mohammed, A. A., Hussein, S. A. M., Ahmed, M. A., Saad, A., & Raoof, M. In-Silico Study of Destabilizing Alzheimer’s Aβ42 Protofibrils With Curcumin.