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The retinoic acid receptor alpha (RARA) gene is not associated with myopia, hypermetropia, and ocular biometric measures.

Veerappan S, Schäche M, Pertile KK, Islam FM, Chen CY, Mitchell P, Dirani M, Baird PN - Mol. Vis. (2009)

Bottom Line: Five tag single nucleotide polymorphisms (tSNPs) in RARA with an r(2) of 0.8 and a minor allele frequency greater than 5% were selected for genotyping.We did not identify any significant association between tSNPs in RARA with either myopia or hypermetropia as qualitative traits.Neither did we identify any significant associations of these tSNPs with the quantitative traits of axial length, corneal curvature and anterior chamber depth.

View Article: PubMed Central - PubMed

Affiliation: Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, 32 Gisborne Street, East Melbourne 3002, Australia.

ABSTRACT

Purpose: The Retinoic Acid Receptor Alpha (RARA) gene is a potential candidate gene for myopia due to its differential expression in animal models during experimentally induced myopia. To test for whether RARA is associated with myopia we have undertaken a case-control study assessing for associations between RARA and myopia, hypermetropia, and ocular biometric measures.

Methods: A total of 802 Anglo-Celtic individuals were genotyped. Five tag single nucleotide polymorphisms (tSNPs) in RARA with an r(2) of 0.8 and a minor allele frequency greater than 5% were selected for genotyping. Genotype frequencies of these 5 tSNPs were compared between individuals with emmetropia and those with myopia or hypermetropia. A quantitative analysis was also performed to assess associations with ocular biometric measures including axial length, corneal curvature and anterior chamber depth.

Results: We did not identify any significant association between tSNPs in RARA with either myopia or hypermetropia as qualitative traits. Neither did we identify any significant associations of these tSNPs with the quantitative traits of axial length, corneal curvature and anterior chamber depth.

Conclusions: This is the first study to assess for associations between RARA and myopia, hypermetropia, and ocular biometric measures. Our findings suggest that variations in the nucleotide sequence of RARA are not associated with myopia, hypermetropia, or ocular biometric measures in our population.

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Related in: MedlinePlus

Linkage disequilibrium (LD) map comparing the current study with HapMap data for single nucleotide polymorphisms in the RARA gene. In the left hand panel is shown the LD block with r2 values indicated in the red diamonds and the position of the 5 tag SNPs for the current study. In the right hand panel the LD map from available HapMap data with position of available SNPs as well as the 5 tag SNPs (r2 values are indicated in the diamonds).  At the top of the panel are shown the different RARA alternatively spliced transcripts at this location on chromosome 17 (http://genome.ucsc.edu/).
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f2: Linkage disequilibrium (LD) map comparing the current study with HapMap data for single nucleotide polymorphisms in the RARA gene. In the left hand panel is shown the LD block with r2 values indicated in the red diamonds and the position of the 5 tag SNPs for the current study. In the right hand panel the LD map from available HapMap data with position of available SNPs as well as the 5 tag SNPs (r2 values are indicated in the diamonds). At the top of the panel are shown the different RARA alternatively spliced transcripts at this location on chromosome 17 (http://genome.ucsc.edu/).

Mentions: All five SNPs for the population under study where in high LD with each other (r2 <0.95) with the exception of rs4890109 which is not in high lD with rs9303285. All five SNPs studies in this population fall within the same LD block. This is comparable, but not identical , to the HapMap data from the CEU population which places rs4890109 in a different LD block to the other four SNPs (Figure 2). Haplotype analysis was undertaken using a two, three, four, or five sliding SNP window to investigate haplotype associations. No significant associations were observed based on this analysis and was similar to that obtained from analysis when using single SNPs.


The retinoic acid receptor alpha (RARA) gene is not associated with myopia, hypermetropia, and ocular biometric measures.

Veerappan S, Schäche M, Pertile KK, Islam FM, Chen CY, Mitchell P, Dirani M, Baird PN - Mol. Vis. (2009)

Linkage disequilibrium (LD) map comparing the current study with HapMap data for single nucleotide polymorphisms in the RARA gene. In the left hand panel is shown the LD block with r2 values indicated in the red diamonds and the position of the 5 tag SNPs for the current study. In the right hand panel the LD map from available HapMap data with position of available SNPs as well as the 5 tag SNPs (r2 values are indicated in the diamonds).  At the top of the panel are shown the different RARA alternatively spliced transcripts at this location on chromosome 17 (http://genome.ucsc.edu/).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2713734&req=5

f2: Linkage disequilibrium (LD) map comparing the current study with HapMap data for single nucleotide polymorphisms in the RARA gene. In the left hand panel is shown the LD block with r2 values indicated in the red diamonds and the position of the 5 tag SNPs for the current study. In the right hand panel the LD map from available HapMap data with position of available SNPs as well as the 5 tag SNPs (r2 values are indicated in the diamonds). At the top of the panel are shown the different RARA alternatively spliced transcripts at this location on chromosome 17 (http://genome.ucsc.edu/).
Mentions: All five SNPs for the population under study where in high LD with each other (r2 <0.95) with the exception of rs4890109 which is not in high lD with rs9303285. All five SNPs studies in this population fall within the same LD block. This is comparable, but not identical , to the HapMap data from the CEU population which places rs4890109 in a different LD block to the other four SNPs (Figure 2). Haplotype analysis was undertaken using a two, three, four, or five sliding SNP window to investigate haplotype associations. No significant associations were observed based on this analysis and was similar to that obtained from analysis when using single SNPs.

Bottom Line: Five tag single nucleotide polymorphisms (tSNPs) in RARA with an r(2) of 0.8 and a minor allele frequency greater than 5% were selected for genotyping.We did not identify any significant association between tSNPs in RARA with either myopia or hypermetropia as qualitative traits.Neither did we identify any significant associations of these tSNPs with the quantitative traits of axial length, corneal curvature and anterior chamber depth.

View Article: PubMed Central - PubMed

Affiliation: Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, 32 Gisborne Street, East Melbourne 3002, Australia.

ABSTRACT

Purpose: The Retinoic Acid Receptor Alpha (RARA) gene is a potential candidate gene for myopia due to its differential expression in animal models during experimentally induced myopia. To test for whether RARA is associated with myopia we have undertaken a case-control study assessing for associations between RARA and myopia, hypermetropia, and ocular biometric measures.

Methods: A total of 802 Anglo-Celtic individuals were genotyped. Five tag single nucleotide polymorphisms (tSNPs) in RARA with an r(2) of 0.8 and a minor allele frequency greater than 5% were selected for genotyping. Genotype frequencies of these 5 tSNPs were compared between individuals with emmetropia and those with myopia or hypermetropia. A quantitative analysis was also performed to assess associations with ocular biometric measures including axial length, corneal curvature and anterior chamber depth.

Results: We did not identify any significant association between tSNPs in RARA with either myopia or hypermetropia as qualitative traits. Neither did we identify any significant associations of these tSNPs with the quantitative traits of axial length, corneal curvature and anterior chamber depth.

Conclusions: This is the first study to assess for associations between RARA and myopia, hypermetropia, and ocular biometric measures. Our findings suggest that variations in the nucleotide sequence of RARA are not associated with myopia, hypermetropia, or ocular biometric measures in our population.

Show MeSH
Related in: MedlinePlus