Computational protocol: Association between ST8SIA2 and the Risk of Schizophrenia and Bipolar I Disorder across Diagnostic Boundaries

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Protocol publication

[…] We used the Korean Hapmap database (http://www.khapmap.org) to select ST8SIA2 tag SNPs. Thirty-one tag SNPs were chosen by the program Tagger within Haploview v4.0 (http://www.broad.mit.edu/mpg/haploview) using pairwise tagging of SNPs with an r2 > 0.8 and minor allele frequency (MAF) > 0.05 [, ]. An additional three SNPs (rs3759916, rs3759915, and rs3759914), which previously showed a significant association with schizophrenia [, ] in other Asian populations, were included in the analysis. The selected SNPs and their genomic or intragenic location, allele types, and minor allele frequencies are summarized in . All SNPs were intronic, except rs3759916, rs3759915, and rs3759914 on the 5′-untranslated region (UTR) and rs2290492 and rs17600420 on the 3′-UTR. These SNPs spanned the entire ST8SIA2 gene with an average inter-SNP distance of 2.2 kb (range, 56 bp–12.7 kb). [...] Whole blood was collected from each individual into EDTA tubes, and genomic DNA was isolated from peripheral blood leukocytes using the Wizard Genomic DNA Purification kit according to the manufacturer’s instructions (Promega, Madison, WI, USA). MassARRAY Assay Design, version 3.0 software (Sequenom Inc, San Diego, CA, USA) generated three multiplex reactions: 12 SNPs (plex 1), 12 SNPs (plex 2), and 10 SNPs (plex 3). Multiplex SNP genotyping was performed by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using the iPLEX Gold technology from Sequenom. SNP assays were designed using Sequenom MassARRAY Assay Design ver. 3.0 software (primer information is available upon request). The polymerase chain reaction was performed according to the standard iPLEX methodology. Spectra were analyzed by MassARRAY Typer ver. 3.4 software (Sequenom). Quality control was performed to exclude individual SNPs or samples with genotype call rates < 95% and SNP assays with poor-quality spectra/cluster plots.To confirm the reliability of iPLEX SNP genotyping method, five selected SNPs (rs4777973, rs3784731, rs11637898, rs1455777, and rs897463) for 48 random samples were regenotyped by sequencing reaction using ABI PRISM BigDye Terminator v 3.1 Cycle Sequencing Kits (Applied Biosystems, CA, USA) The concordance rate of genotype data between sequencing and iPLEX SNP genotyping was 99.2% [...] We used the Kruskal–Wallis test or the chi-square test to reveal differences in demographic variables among the patient and control groups. The Hardy–Weinberg equilibrium was checked with Fisher’s exact test for the genetics analysis, and no significant deviation was observed in any of the SNPs (). Genotype-wise association was evaluated by logistic regression analysis with age and sex as covariates. Additive, dominant, and recessive genetic models were considered based on the minor allele of each SNP. The inheritance model with the least Akaike Information Criterion [] was accepted as the best fitting model. We controlled the experiment-wise type I error using the Bonferroni correction. Thirty-four SNPs were analyzed; thus, a p-value = 0.0015 (0.05/34) was the adjusted level of significance. All statistical analyses were done with snpStats ver. 1.18.0 in R ver. 3.0.2 (http://www.bioconductor.org) []. […]

Pipeline specifications

Software tools Tagger, Haploview, MassArray, snpStats
Application GWAS
Organisms Homo sapiens
Diseases Genetic Diseases, Inborn