An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C9*3 (rs1057910)

This thesis is submitted in partial fulfilment of the requirements for the degree of Bachelor of Science in Biotechnology 2020.

Detalhes bibliográficos
Autor principal:	Ahmed, Rifaquat
Outros Autores:	Hossain, M. Mahboob
Formato:	Thesis
Idioma:	en_US
Publicado em:	Brac University 2021
Assuntos:	SNP genotyping protocol Single Nucleotide Polymorphisms Drug Metabolizing Gene Tetra-primer
Acesso em linha:	http://hdl.handle.net/10361/14388

id	10361-14388
record_format	dspace
spelling	10361-143882021-03-24T21:01:17Z An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C93 (rs1057910) Ahmed, Rifaquat Hossain, M. Mahboob Akash, Md. Mahmudul Hasan Department of Mathematics and Natural Sciences, Brac University SNP genotyping protocol Single Nucleotide Polymorphisms Drug Metabolizing Gene Tetra-primer This thesis is submitted in partial fulfilment of the requirements for the degree of Bachelor of Science in Biotechnology 2020. Catalogued from PDF version of thesis. Includes bibliographical references (pages 57-62). The role of SNP is an important factor related to drug metabolism. The presence or absence of SNP can significantly alter the effect of the same amount of drug inside the body leading to various unwanted side-effects which can be harmful at times. The drug warfarin is one such drug that has a different effect based on the SNPs present inside the CYP2C9 gene metabolizing the drug. Various SNPs can be present at different positions in the CYP2C9 gene among which some of them can be in the active site which has a significant impact on drug metabolism. However, not all SNPs can have an effect on drug metabolism. As a result, bioinformatics tools were used in the study to identify the clinically significant SNPs from the CYP2C9 gene. Homology based modeling was used to model 3D proteins containing candidate SNPs which were docked with the ligand to be compared with positive control. The results showed data that could be used for comparison to know significant SNPs in the CYP2C9 gene. The CYP2C93 was found to be a clinically significant SNP that has a prevalence in the Bangladeshi population. Then, for the determination of the genotypes in the collected samples, a method was required for genotyping. There are various methods for genotyping of a SNP among which the tetra primer ARMS-PCR method was selected due to the process being inexpensive, time-efficient, and easy to perform in any diagnostic labs across the country. The primers were designed using a web-based primer designing tool and the PCR process was optimized for a successful PCR reaction. The optimization was successful which showed bands in the gel electrophoresis. However, due to the sample number being low, even though there were the bands for the outer primer and the band for wild type allele, no bands for mutant alleles were obtained. Thus, the prevalence of the mutant allele could not be confirmed. Further experimentation on more samples is required to obtain enough data to know the prevalence of mutant alleles in the population using the optimized PCR method. Rifaquat Ahmed B. Biotechnology 2021-03-24T10:01:17Z 2021-03-24T10:01:17Z 2020 2020-08 Thesis ID: 16136027 http://hdl.handle.net/10361/14388 en_US Brac University theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. 62 pages application/pdf Brac University
institution	Brac University
collection	Institutional Repository
language	en_US
topic	SNP genotyping protocol Single Nucleotide Polymorphisms Drug Metabolizing Gene Tetra-primer
spellingShingle	SNP genotyping protocol Single Nucleotide Polymorphisms Drug Metabolizing Gene Tetra-primer Ahmed, Rifaquat An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C9*3 (rs1057910)
description	This thesis is submitted in partial fulfilment of the requirements for the degree of Bachelor of Science in Biotechnology 2020.
author2	Hossain, M. Mahboob
author_facet	Hossain, M. Mahboob Ahmed, Rifaquat
format	Thesis
author	Ahmed, Rifaquat
author_sort	Ahmed, Rifaquat
title	An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C9*3 (rs1057910)
title_short	An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C9*3 (rs1057910)
title_full	An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C9*3 (rs1057910)
title_fullStr	An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C9*3 (rs1057910)
title_full_unstemmed	An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C9*3 (rs1057910)
title_sort	in silico approach for the identification of clinically significant snps in a drug metabolizing gene cyp2c9 and development of tetra-primer arms pcr based genotyping method for cyp2c9*3 (rs1057910)
publisher	Brac University
publishDate	2021
url	http://hdl.handle.net/10361/14388
work_keys_str_mv	AT ahmedrifaquat aninsilicoapproachfortheidentificationofclinicallysignificantsnpsinadrugmetabolizinggenecyp2c9anddevelopmentoftetraprimerarmspcrbasedgenotypingmethodforcyp2c93rs1057910 AT ahmedrifaquat insilicoapproachfortheidentificationofclinicallysignificantsnpsinadrugmetabolizinggenecyp2c9anddevelopmentoftetraprimerarmspcrbasedgenotypingmethodforcyp2c93rs1057910
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An in silico approach for the identification of clinically significant SNPs in a Drug Metabolizing Gene CYP2C9 and development of Tetra-primer ARMS PCR based genotyping method for CYP2C9*3 (rs1057910)

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