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Chunk #15 — MATERIALS AND METHODS — Tag SNP Selection and Genotyping

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Limited associations of dopamine system genes with alcohol dependence and related traits in the Irish Affected Sib Pair Study of Alcohol Dependence (IASPSAD).
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tSNPs were genotyped in-house as monoplex reactions using Taqman Assays-on-Demand (Applied Biosystems, Foster City, CA). To ensure uniformity and accuracy, all reaction steps were performed using the Eppendorf 5075 automated liquid-handling platform. Stringent evaluation of initial data is important to avoid artifactual effects of genotyping errors; therefore, all genotypes were independently assessed by two raters. Ambiguous calls were discussed and in cases of non-resolution, genotypes were dropped from the analyses. Individual DNA samples with 20% or more missing genotypes across the entire study were also excluded. Individual SNPs were excluded if they showed deviation from Hardy–Weinberg equilibrium (using a regular cut-off p-value of 0.001) in the overall sample and controls alone, had an MAF < 1%, or had a low genotyping call rate (<80%). The present study reports on the results from genes included in the DA functional domain (Hodgkinson et al., 2008), including DRD1–5, SLC18A2, SLC6A3, DDC, TH, and COMT. Several coding SNPs were genotyped, such as rs155417 and rs5326 in DRD1, rs6279 in DRD2, rs6347 in SLC6A3, rs11575542 and rs11575377 in DDC, and the well-studied nonsynonymous SNP rs4680