Peripheral blood samples were collected from SZ and healthy controls by using evacuated tubes containing EDTA anticoagulant. RelaxGene Blood DNA System (Tiangen Biotech, Beijing, China) was used to extract genomic DNA from white blood cells. The method of genotyping was described in our previous studies that use the Illumina GoldenGate assays on a BeadStation 500G Genotyping System (Illumina, San Diego, CA, USA) (3 (link), 12 (link), 25 (link)).
Beadstation 500g genotyping system
Manufactured by Illumina
Sourced in United States
The BeadStation 500G Genotyping System is a high-throughput genotyping platform designed for large-scale genetic analysis. The system enables efficient processing of DNA samples and generates genotype data for genetic markers across the genome.
Automatically generated - may contain errors
4 protocols using beadstation 500g genotyping system
1
Genomic DNA Extraction and Genotyping
2
Genomic DNA Extraction and Genotyping
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Peripheral blood samples were collected from all subjects using evacuated tubes containing EDTA anticoagulant. Genomic DNA was extracted from white blood cells using the RelaxGene Blood DNA System (Tiangen Biotech, Beijing, China). Genotyping was performed using Illumina GoldenGate assays on a BeadStation 500G Genotyping System (Illumina, San Diego, CA, USA) in stage 1 per our previous studies (5 (link), 22 (link), 26 (link)). The llumina 660K Genotyping System was using to genotyping in stage 2.
3
Illumina Genotyping Quality Control
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Genotyping was performed using Illumina GoldenGate assays on a BeadStation 500G Genotyping System (Illumina, Inc., San Diego, CA, USA). DNA samples (250 ng) were genotyped according to the Illumina protocol. DNA samples from cases and controls were randomly sorted, including 96 duplicated DNA samples for genotyping quality control. Genotype calls were made using the Genotyping module of the BeadStudio 2.0 software (Illumina, Inc.). All genotype data were examined for cluster separation using Illumina quality scores generated by the software. Poorly performing SNPs were excluded, designated by a GenTrain score <0.4 or a cluster separation score <0.6. SNPs were further excluded from controls not in Hardy–Weinberg equilibrium (HWE). As a genotyping quality control, four SNPs were genotyped in duplicate (100 samples) by DNA sequencing.
4
Genetic Variation Analysis of ARHGAP18
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A peripheral blood sample was drawn from each subject into vacutainer tubes containing the anticoagulant ethylenediaminetetraacetic acid. Genomic DNA was extracted from leukocytes using the RelaxGene Blood DNA System (Tiangen Biotech., Beijing, China). In the discovery stage, the genotypes of 35 SNPs in ARHGAP18 were evaluated using the Illumina GoldenGate assay on a BeadStation 500G Genotyping System (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s instructions.
Validation of specific SNPs, including rs9483050, rs7758025, rs12197901, and rs9492347, was performed using the TaqMan genotyping method according to the manufacturer’s protocol, with allelic discrimination and analysis performed on an ABI Prism 7900 Sequence Detection System (Applied Biosystems, Foster City, CA, USA). The ABI Taqman probe sequences are listed inS1 Table . To evaluate the quality of genotyping, 5% of the samples were randomly selected and re-genotyped. The genotyping consistency rate was more than 98%.
Validation of specific SNPs, including rs9483050, rs7758025, rs12197901, and rs9492347, was performed using the TaqMan genotyping method according to the manufacturer’s protocol, with allelic discrimination and analysis performed on an ABI Prism 7900 Sequence Detection System (Applied Biosystems, Foster City, CA, USA). The ABI Taqman probe sequences are listed in
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