Computational protocol: Epistatic and gene wide effects in YWHA and aromatic amino hydroxylase genes across ADHD and other common neuropsychiatric disorders: Association with YWHAE

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Protocol publication

[…] The markers in TPH1 and TPH2 were chosen from previous candidate gene studies performed by our group as well as others [Johansson et al., ; Gao et al., ]. All YWHA‐genes and TH were tagged using the aggressive tagging algorithm with default settings of Haploview, based on CEU data from the HapMap release 28 [International HapMap Consortium, ; Barrett et al., ]. Each gene was tagged with approximately 5,000 basepair flanking sequence included.Genotyping was done in two batches using MassArray iPlex system (Sequenom, San Diego, CA) at CIGENE center for genotyping (University of Life Sciences, Ås, Norway). The genotyping of all selected SNPs was attempted in the first batch. Genes containing failed or low quality SNPs in the first batch were re‐tagged using the “force exclude” and “force include” functions of Haploview and the new tagging SNPs were genotyped in the second batch. There was no SNP‐overlap between the two batches. To assess the genotyping concordance within each of the two batches, two internal controls were used with a total number of 83 duplicates of the two samples.Genotyping quality control (QC) was done in PLINK for each batch separately, and then again after combining the two batches [Purcell et al., ]. The inclusion criteria was defined as individual and SNP genotyping rate above 95%, minor allele frequency (MAF) above 5% in controls and a Hardy–Weinberg disequilibrium threshold of P > 0.01 in controls. [...] Single SNP‐based interaction analyses were performed in the form of likelihood ratio tests implemented in SNPassoc package [González et al., ]. SNPassoc was carried out in R‐software, using gender as a covariate, testing for association with aADHD status (www.r‐project.org). Only interaction between genes was evaluated, meaning that each SNP was tested for interaction with all SNPs in other genes, but not with SNPs in the same gene. Thus, in total, 495 interaction SNP pairs were tested in this study.In order to further explore the strongest epistasis observed, we performed logistic regressions with the two‐way interaction term between the pair of SNPs revealing the signal. The regressions were performed in R software.Bonferroni correction for 495 SNP interaction tests was used to adjust for multiple testing, resulting in the corrected significance threshold of 1.01E‐04.To evaluate the power of our study to detect a true association, basic power calculations was performed using the Genetic Power Calculator, applying the sample size of our data to a single SNP with minor allele frequency of 0.1 and 0.2 and a genotype relative risk (GRR) of 1.5, given ADHD disease prevalence of 3% [Purcell et al., ]. […]

Pipeline specifications

Software tools Haploview, PLINK, SNPassoc
Application GWAS
Organisms Homo sapiens
Chemicals Catecholamines, Serotonin, Tryptophan, Tyrosine