5、6号染色体上SNP位点与高度近视的关联研究
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摘要
目的本实验拟研究5、6号染色体上位点(rs575425, rs492842, rs7706272, rs6895664, rs10484791和rs2073135)的单核苷酸多态性(single nucleotide polymorphism, SNP),研究其与中国汉族人群高度近视的关联性。
方法通过全基因组扫描选取5、6号染色体上的6个阳性SNPs (rs575425, rs492842, rs7706272, rs6895664, rs10484791和rs2073135)。选择506例高度近视患者和991例正常健康者(均为中国汉族),收集其外周血标本并提取标本DNA。根据上述6个位点相应序列设计上、下游扩增引物和SNaPshot引物,用聚合酶链反应(polymerase chain reaction, PCR)进行DNA扩增,用不同荧光标记的ddNTP对PCR产物进行一步延伸,然后置于310型DNA测序仪上检测基因型,即SNaPshot技术。对检测的结果进行Hardy—Weinberg平衡检验、卡方检验、连锁不平衡分析及单倍体分析,判断6个SNPs与高度近视易感性之间的关系。
结果6个SNP位点的基因型都符合Hardy-Weinberg平衡(P>0.05)。rs10484791和rs2073135位点的等位基因频率和基因型频率在高度近视组和对照组间差别有统计学意义(P<0.05). rs575425, rs492842, rs7706272和rs6895664位点等位基因频率和基因型频率在高度近视组和对照组间差异没有统计学意义(P>O.05)。rs10484791和rs2073135都位于脑组织特异性血管生成抑制因子3(brain-specific angiogenesis inhibitor-3, BAI3)基因区域,且位于连锁不平衡区域。单倍体型H1 (CG)和单倍体型H2(TA)在高度近视组和对照组间差异有统计学意义(P<0.05)。
结论BAI3基因的rs10484791和rs2073135位点与中国汉族人群高度近视相关。
Objective:To study the association between the single nucleotide polymorphisms in chromosome 5 and chromosome 6 (rs575425, rs492842, rs7706272, rs6895664, rs10484791 and rs2073135) and high myopia in Chinese Han population.
Methods: Six positive SNPs (rs575425, rs492842, rs7706272, rs6895664, rs10484791 and rs2073135) in chromosome 5 and 6 were selected by genome-wide scaning. Peripheral blood samples from 506 patients with high myopia and 991 healthy controls were collected respectively and genome DNA of them were extracted. All paticipants were Chinese Han population. Two specific primers and specific primers of SNaPshot were designed to corresponding gene region involved in the six positive SNPs. Polymerase chain reaction was used to amplify genome DNA, diferent fluorescent dye labeled ddNTP was used to further extend the strand of PCR product, then the genotypes were detected by ABI 3130XL-Avant Genetic Analyzer. This is SNaPshot technique. Statistical analysis, including Hardy—Weinberg equilibrium test, Chi-square test, linkage disequilibrium analysis and haplotype analysis were performed to determine the association between the SNPs and the susceptibility of high myopia.
Results:All the genotype frequencies of the six SNPs were in Hardy-Weinberg equilibrium (P>0.05). The allele and genotype frequencies of rs 10484791 and rs2073135 polymorphism in high myopia patients were significantly different from those of the healthy controls(P<0.05). There were not significant differences in allele and genotype frequencies of rs575425, rs492842, rs7706272 and rs6895664 between high myopia patients and healthy controls (P> 0.05). Moreover, rs10484791 and rs2073135 both locate in BAI3 (brain-specific angiogenesis inhibitor-3) gene block, except for in linkage disequilibrium block. Haplotypes H1(CG) and H2(TA) in the high myopia patients were significantly different from those of healthy controls(P<0.05).
Conclusion:BA13 gene polymorphisms (rs10484791 and rs2073135) are highly associated with high myopia in Chinese Han population.
方法通过全基因组扫描选取5、6号染色体上的6个阳性SNPs (rs575425, rs492842, rs7706272, rs6895664, rs10484791和rs2073135)。选择506例高度近视患者和991例正常健康者(均为中国汉族),收集其外周血标本并提取标本DNA。根据上述6个位点相应序列设计上、下游扩增引物和SNaPshot引物,用聚合酶链反应(polymerase chain reaction, PCR)进行DNA扩增,用不同荧光标记的ddNTP对PCR产物进行一步延伸,然后置于310型DNA测序仪上检测基因型,即SNaPshot技术。对检测的结果进行Hardy—Weinberg平衡检验、卡方检验、连锁不平衡分析及单倍体分析,判断6个SNPs与高度近视易感性之间的关系。
结果6个SNP位点的基因型都符合Hardy-Weinberg平衡(P>0.05)。rs10484791和rs2073135位点的等位基因频率和基因型频率在高度近视组和对照组间差别有统计学意义(P<0.05). rs575425, rs492842, rs7706272和rs6895664位点等位基因频率和基因型频率在高度近视组和对照组间差异没有统计学意义(P>O.05)。rs10484791和rs2073135都位于脑组织特异性血管生成抑制因子3(brain-specific angiogenesis inhibitor-3, BAI3)基因区域,且位于连锁不平衡区域。单倍体型H1 (CG)和单倍体型H2(TA)在高度近视组和对照组间差异有统计学意义(P<0.05)。
结论BAI3基因的rs10484791和rs2073135位点与中国汉族人群高度近视相关。
Objective:To study the association between the single nucleotide polymorphisms in chromosome 5 and chromosome 6 (rs575425, rs492842, rs7706272, rs6895664, rs10484791 and rs2073135) and high myopia in Chinese Han population.
Methods: Six positive SNPs (rs575425, rs492842, rs7706272, rs6895664, rs10484791 and rs2073135) in chromosome 5 and 6 were selected by genome-wide scaning. Peripheral blood samples from 506 patients with high myopia and 991 healthy controls were collected respectively and genome DNA of them were extracted. All paticipants were Chinese Han population. Two specific primers and specific primers of SNaPshot were designed to corresponding gene region involved in the six positive SNPs. Polymerase chain reaction was used to amplify genome DNA, diferent fluorescent dye labeled ddNTP was used to further extend the strand of PCR product, then the genotypes were detected by ABI 3130XL-Avant Genetic Analyzer. This is SNaPshot technique. Statistical analysis, including Hardy—Weinberg equilibrium test, Chi-square test, linkage disequilibrium analysis and haplotype analysis were performed to determine the association between the SNPs and the susceptibility of high myopia.
Results:All the genotype frequencies of the six SNPs were in Hardy-Weinberg equilibrium (P>0.05). The allele and genotype frequencies of rs 10484791 and rs2073135 polymorphism in high myopia patients were significantly different from those of the healthy controls(P<0.05). There were not significant differences in allele and genotype frequencies of rs575425, rs492842, rs7706272 and rs6895664 between high myopia patients and healthy controls (P> 0.05). Moreover, rs10484791 and rs2073135 both locate in BAI3 (brain-specific angiogenesis inhibitor-3) gene block, except for in linkage disequilibrium block. Haplotypes H1(CG) and H2(TA) in the high myopia patients were significantly different from those of healthy controls(P<0.05).
Conclusion:BA13 gene polymorphisms (rs10484791 and rs2073135) are highly associated with high myopia in Chinese Han population.
引文
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