Computational protocol: Lack of Association between the TSPAN18 Gene and Schizophrenia Based on New Data from Han Chinese and a Meta-Analysis

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Protocol publication

[…] In the current study, we conducted preliminary analysis using the HapMap data to select the transcription unit (including the 5'UTR, exons, and 3'UTR regions) of the TSPAN18 gene regions tagSNPs. The selected tagSNPs met the following criteria []. First, we examined tagSNPs in Haploview (v4.2) using the CHB (Chinese Han Beijing) population and a minor allele frequency cut-off (MAF) > 5%. Second, a MAF > 20% with pair-wise tagging and R2 > 0.8 [] were used as cut-off for the selection of tagSNPs. Ultimately, seven SNPs (rs11038167, intron 2; rs11038172, intron 2; rs835990, intron 8; rs704671, exon10; rs73456450, exon10; rs836001, exon10; and rs836002, exon10) were selected for genotyping and analyses.Human genomic DNA was extracted according to the manufacturer’s recommendations (Omiga, Bio-tek, Norcross, GA, USA). All SNPs were genotyped with the SNPscan technique using SNPscan™ kit (Genesky Biotechnologies Inc., Shanghai, China) to design and determine the genotypes. This is a high-throughput and cost-saving SNP genotyping method based on double ligation and multiplex fluorescence PCR [,], and its high accuracy has been validated by many studies [,]. Five percent of the high DNA quality samples were randomly subjected to repeated analyses to guarantee the genotyping qualities. The average genotype call rate for all markers was 96%. [...] The statistic power of our sample size was calculated with the G*Power program (Franz Faul, University Kiel, Kiel, Germany), according to Cohen’s method []. The sample size indicated a > 90% power to detect significant (a < 0.05) associations of alleles, genotypes and haplotypes at an effect size of 0.1 (which corresponds to a “weak” gene effect).The genotype, allele and haplotype frequency differences between the cases and controls were calculated with chi-square test, which was also used to estimate whether the SNP genotypes deviated from the expected Hardy–Weinberg equilibrium (HWE) values. Logistic regression analyses were selected to identify the SCZ-associated SNPs according to the odds ratios (OR), 95% confidence intervals (CIs), and corresponding p-values. Moreover, the analyses of single SNPs were performed using the following multiple inheritance models: the additive, dominant model (the minor allele homozygotes plus the heterozygotes vs. the major allele homozygotes), and a recessive model (the minor allele homozygotes vs. the heterozygotes plus the major allele homozygotes).Partitioning of the linkage disequilibrium (LD) blocks was performed with Haploview 4.2 []. All statistical analyses were performed with PLINK (version 1.07) []. Differences were considered significant when the p value was <0.007 after Bonferroni correction (0.05/7). […]

Pipeline specifications

Software tools Haploview, OMIGA, G*Power, PLINK
Applications Miscellaneous, GWAS
Organisms Homo sapiens
Chemicals Calcium, Dopamine