Screening sequence variations by high resolution melting analysis and investigating the role of opticin gene (OPTC) rare variants in high myopia

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Screening sequence variations by high resolution melting analysis and investigating the role of opticin gene (OPTC) rare variants in high myopia

 

Author: Jap, Ching-pui Becky
Title: Screening sequence variations by high resolution melting analysis and investigating the role of opticin gene (OPTC) rare variants in high myopia
Degree: M.Sc.
Year: 2010
Subject: Hong Kong Polytechnic University -- Dissertations
Myopia -- Genetic aspects
Myopia -- Etiology.
Polymerase chain reaction
Gene amplification
Department: Dept. of Health Technology and Informatics
Pages: xvi, 122 leaves : col. ill. ; 31 cm.
InnoPac Record: http://library.polyu.edu.hk/record=b2391078
URI: http://theses.lib.polyu.edu.hk/handle/200/5856
Abstract: development of myopia is still unclear. The excessive growth of the eyeball, leading to the excessive axial length of the eye was commonly found in juvenile onset myopia. Although the underlying aetiology is still controversial, many research studies tried to map the genes of myopia at the molecular basis. Opticin was found to be one of the small leucine-rich repeat proteins/proteoglycans which makes up extracellular matrix in the vitreous. OPTC, the gene coding for opticin is selected for this association study. A previous English study observed higher numbers of rare variations in OPTC in cases than in controls. Chinese samples, 300 highly myopic cases and 300 emmetropic controls were used in this study to see whether rare variations were also observed in the Chinese population. Polymerase chain reaction was carried out to amplify 7 exons of OPTC and high resolution melting (HRM) analysis used to screen for the rare variants in the amplified products. With the use of Lightcycler LC 480 and the DNA saturating dye Syto 9, rare variants in the 7 exons were screened by HRM. All suspected rare variants detected in HRM were sequenced to confirm the screening. In total, 24 samples with 11 mutation sites were detected in this study and all of them were heterozygous single nucleotide mutations. Four of the mutations detected were documented in dbSNP of NCBI while seven were novel. PolyPhen-2, an online tool, was used to predict the effect of amino acid change on the protein level. Six out of the 8 amino acid variations in the OPTC rare variants were found to be "probably damaging" or "possibly damaging" to opticin although the difference of allele frequencies between cases and controls were not significant in this study.

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