研究目的
To identify genetic factors influencing individual differences in susceptibility to central serous chorioretinopathy (CSC) in the Japanese population.
研究成果
The study identified rs11865049 in the SLC7A5 gene as a novel susceptibility locus for CSC in the Japanese population, with a combined P value of 9.71 × 10^-9 and odds ratio of 2.10. This suggests SLC7A5 as a potential candidate gene, indicating a new molecular mechanism for CSC. The findings contribute to understanding the pathogenesis of CSC, but further studies are needed to confirm and explore functional effects.
研究不足
The use of imputed data in the replication study might cause false-positive or false-negative results. The sample size might not provide sufficient power to find more SNPs associated with CSC. The study was limited to a single race (Japanese), so replication in other races is needed. DNA sequencing or imputation for all SNPs was not performed, potentially missing other associated variants.
1：Experimental Design and Method Selection:
A two-stage genome-wide association study (GWAS) was conducted, involving a discovery stage and a replication stage, followed by meta-analysis to identify genetic associations with CSC. The Cochran-Armitage trend test was used for association analysis, and quality control procedures were applied to exclude low-quality SNPs.
2：Sample Selection and Data Sources:
The study included 320 unrelated Japanese idiopathic CSC cases and 3245 population-based controls. Cases were diagnosed based on detailed ophthalmic examinations, including slit-lamp biomicroscopy, color fundus photography, fluorescein angiography, indocyanine green angiography, and spectral-domain optical coherence tomography. Controls were population-based volunteers from various sources.
3：List of Experimental Equipment and Materials:
Genomic DNA was extracted using a blood DNA kit (QIAGEN). Genotyping was performed using Illumina Human Omni Express BeadChips and TaqMan SNP Genotyping Assays on a StepOnePlus Real-Time PCR System. Software tools included PLINK, EIGENSOFT, SHAPEIT2, Minimac3, Haploview, SNPinfo, SNPnexus, LDlink, and the Human Genetic Variation database.
4：Experimental Procedures and Operational Workflow:
DNA extraction, genotyping, quality control (excluding SNPs with low call rate, Hardy-Weinberg equilibrium P < threshold, minor allele frequency < threshold), association testing using CATT, replication study with additional samples, and meta-analysis combining results.
5：Data Analysis Methods:
Statistical analyses were performed using PLINK for association tests, meta-analysis, and calculation of odds ratios and confidence intervals. Functional annotation of SNPs was predicted using web servers like SNPinfo and SNPnexus.
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