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Y.-J. Li, A. Dellinger, T. L. Young, S. M. Saw; Copy Number Variant Survey in Myopia of Singapore Chinese Schoolchildren. Invest. Ophthalmol. Vis. Sci. 2009;50(13):2568.
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Copy number variants (CNVs), duplications or deletions of chromosomal segments, are common in the human genome and can be used as genetic markers for disease studies. CNV data can be generated by multiple platforms, including high density single nucleotide polymorphism (SNP) arrays. Here, we compare the distribution of SNP array derived CNVs among different refractive error statuses using 959 Chinese aged 7 to 9 years at baseline from the Singapore Cohort study Of the Risk factors for Myopia (SCORM).
Whole genome SNP genotyping were conducted using Illumina HumanHap 550 Beadchips. CNVs were detected using Nexus CGHTM. A CNV is defined with a minimum of five SNPs within the region detected by Nexus. These SNPs in CNVs are called CNV SNPs. Individuals were grouped by refractive error based on the most recent eye exam and the most severe eye: high myopia (<-6.00 diopter (D), n=102), moderate myopia (-6.00D to -3.00D, n=301), low myopia (-3.00D to -0.50D, n=327), normal (-0.50D to 0.50D, n=128), and hyperopia (> 0.50D, n=101). Multiple descriptive statistics were computed and compared among the five groups, including the mean, median, and standard deviation of the CNV length, and the number and proportion of CNV SNPs and CNVs matched to the database of the confirmed HapMap CNVs. The proportions of CNVs in the myopic groups but not in the normal group were assessed.
The average age of children at the final eye exam is 13.35(SD=1.9). A few samples biased CNV size statistics. With or without these samples, mean and median CNV size is larger in myopia (e.g. 144kb vs. 129kb, 66kb vs. 62kb of high myopia vs. normal, respectively) and increases with myopia severity. More HapMap CNVs and CNV SNPs were found in moderate (2.3%) and high myopia (3.2%) than in normal (1.8%) and hyperopia (1.4%). The percentages of CNVs with sizes >500kb are 19, 20, 6, 16, and 7 for high, moderate, and low myopia, normal and hyperopia, respectively. A high proportion of CNVs in high (42%) and moderate myopia (77%) were not found in the normal group.
Our data in Chinese children show that CNV sizes vary among phenotypic groups, high and moderate myopia having longer CNVs than the normal and hyperopia groups. Higher proportion of CNVs presented only in high or moderate myopia but not normal samples indicating the potential role of CNVs in the development of moderate and high myopia.
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