Dataset Information

Evaluation of BLID and LOC399959 as candidate genes for high myopia in the Chinese Han population.

ABSTRACT: BH3-like motif containing, cell death inducer (BLID) and LOC399959 are two genes associated with the single nucleotide polymorphism (SNP) rs577948, which is a susceptibility locus for high myopia in Japanese subjects. The purpose of this study was to determine if BLID and LOC399959 are associated with high myopia in Chinese Han subjects.High myopia subjects (n=476) had a spherical refractive error of less than -6.00 D in at least one eye and/or an axial length greater than 26 mm. Genomic DNA was extracted and genotyped from peripheral blood leukocytes of high myopes and controls (n=275). Using a case-control association study of candidate regions, linkage disequilibrium blocks for 19 tag SNPs (tSNPs), including rs577948, harbored within and surrounding the BLID and LOC399959 genes were analyzed on a MassArray platform using iPlex chemistry. Each of the tSNPs had an r(2)>0.8 and minor allele frequency >10% in the Chinese Han population. Haplotype association analysis was performed on Haploview 4.1 using Chi-square (?(2)) tests.None of the 19 tSNPs were statistically associated with high myopia.While rs577948 may be associated with high myopia in Japanese subjects, it and the other tSNPs near the BLID and LOC399959 genes are not susceptibility loci for high myopia in the Chinese Han population. Thus, associations of SNPs with high myopia as determined by Genome-Wide Association Study (GWAS) may be restricted to certain ethnic or genetically distinct populations. Without systematic replication in other populations, the results of GWAS associations should be interpreted with great caution.

SUBMITTER: Zhao F

PROVIDER: S-EPMC2956664 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

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Evaluation of BLID and LOC399959 as candidate genes for high myopia in the Chinese Han population.

Zhao Fuxin F Bai Jian J Chen Wei W Xue Anquan A Li Chaohua C Yan Zhonghui Z Chen Hui H Lu Fan F Hu Yongwu Y Qu Jia J Zeng Changqing C Zhou Xiangtian X

Molecular vision 20101002

<h4>Purpose</h4>BH3-like motif containing, cell death inducer (BLID) and LOC399959 are two genes associated with the single nucleotide polymorphism (SNP) rs577948, which is a susceptibility locus for high myopia in Japanese subjects. The purpose of this study was to determine if BLID and LOC399959 are associated with high myopia in Chinese Han subjects.<h4>Methods</h4>High myopia subjects (n=476) had a spherical refractive error of less than -6.00 D in at least one eye and/or an axial length gre ...[more]

PMID: 21031016

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Project description:Background:Fibroblast growth factor 10 (FGF10) is implicated in the growth and development of the eye. Four singles nucleotide polymorphisms (SNPs) in the FGF10 gene (including rs1384449, rs339501, rs12517396 and rs10462070) were found to be associated with extreme myopia (EM, refractive error???-?10.0 diopters) in Japanese and Chinese Taiwan population. This case-control association study was conducted to explore the relationship between these four SNPs and high myopia in a western Chinese population. Methods:A total of 869 high myopia patients (HM, including 485 EM patients) and 899 healthy controls were recruited. These four SNPs were genotyped using the ABI SNaPshot method. Five genetic models (allelic, homozygous, heterozygous, dominant, and recessive) were applied to further evaluate the possible correlation between the SNPs and high myopia. The linkage-disequilibrium block (LD) structure was tested by Haploview Software. Results:In our study, no statistically significant differences were found between HM/EM patients and controls after Bonferroni multiple-correction (P?>?0.05) in the allele frequencies of these four SNPs in the FGF10 gene. We further found that rs12517396AA and rs10462070GG carriers showed a decreased risk of HM/EM compared with rs12517396AC?+?CC and rs10462070GA?+?AA carriers (P?=?0.045, OR?=?0.366; P?=?0.021, OR?=?0.131; P?=?0.03, OR?=?0.341; P?=?0.015, OR?=?0.122; respectively). Additionally, rs12517396AA and rs10462070GG carriers showed the same decreased risk of HM/EM compared with rs12517396CC and rs10462070AA carriers (P?=?0.048, OR?=?0.370; P?=?0.023, OR?=?0.133; P?=?0.032, OR?=?0.346; P?=?0.017, OR?=?0.126). However, these significant associations between rs12517396/rs10462070 and HM/EM disappeared after Bonferroni multiple-correction (P?>?0.05). Conclusion:Our findings indicate that rs12517396 and rs10462070 had marginal association with HM and EM. The other two common polymorphisms in FGF10 unlikely have significant effects in the genetic predisposition to HM/EM in western Chinese population. Further replication studies are needed to validate our findings in both animal models and human genetic epidemiologic studies.

Project description:BackgroundOligozoospermia is one of the severe forms of idiopathic male infertility. However, its pathology is largely unknown, and few genetic factors have been defined. Our previous genome-wide association study (GWAS) has identified four risk loci for non-obstructive azoospermia (NOA).ObjectiveTo investigate the potentially functional genetic variants (including not only common variants, but also less-common and rare variants) of these loci on spermatogenic impairment, especially oligozoospermia.Design setting and participantsA total of 784 individuals with oligozoospermia and 592 healthy controls were recruited to this study from March 2004 and January 2011.MeasurementsWe conducted a two-stage study to explore the association between oligozoospermia and new makers near NOA risk loci. In the first stage, we used next generation sequencing (NGS) in 96 oligozoospermia cases and 96 healthy controls to screen oligozoospermia-susceptible genetic variants. Next, we validated these variants in a large cohort containing 688 cases and 496 controls by SNPscan for high-throughput Single Nucleotide Polymorphism (SNP) genotyping.Results and limitationsTotally, we observed seven oligozoospermia associated variants (rs3791185 and rs2232015 in PRMT6, rs146039840 and rs11046992 in Sox5, rs1129332 in PEX10, rs3197744 in SIRPA, rs1048055 in SIRPG) in the first stage. In the validation stage, rs3197744 in SIRPA and rs11046992 in Sox5 were associated with increased risk of oligozoospermia with an odds ratio (OR) of 4.62 (P ?=? 0.005, 95%CI 1.58-13.4) and 1.82 (P ?=? 0.005, 95%CI 1.01-1.64), respectively. Further investigation in larger populations and functional characterizations are needed to validate our findings.ConclusionsOur study provides evidence of independent oligozoospermia risk alleles driven by variants in the potentially functional regions of genes discovered by GWAS. Our findings suggest that integrating sequence data with large-scale genotyping will serve as an effective strategy for discovering risk alleles in the future.

Dataset Information

Evaluation of BLID and LOC399959 as candidate genes for high myopia in the Chinese Han population.

Publications

Evaluation of BLID and LOC399959 as candidate genes for high myopia in the Chinese Han population.

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