Computational protocol: A DRD2/ANNK1–COMT Interaction, Consisting of Functional Variants, Confers Risk of Post-traumatic Stress Disorder in Traumatized Chinese

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Protocol publication

[…] We chose three important dopaminergic gene loci and their corresponding important functional SNPs, DRD2/ANNK1 (rs1800497 and rs1801028), COMT (rs6269, rs4633, rs4818, and rs4680), and DBH (rs1611115). The detailed information, including chromosome position and possible function, of the SNPs is listed in Supplementary Table . The genotyping was conducted by a custom-by-design 2 × 48-Plex SNPscanTM Kit (Genesky Biotechnologies Inc., Shanghai, China) based on a double ligation and a multiplex fluorescence PCR. A Hardy-Weinberg equilibrium (HWE) test was performed by exact tests of the HWE with efficient computational methods () implemented in PLINK (). The results of the HWE test are shown in Supplementary Table . For our quality control (QC) of the samples, we removed subjects with call rate <0.8. QC of SNPs was performed by excluding SNPs with call rate <0.95 or minor allele frequency (MAF) < 0.01 in either cases or controls or an HWE test P < 0.05 for controls. All the subjects and SNPs passed this standard. [...] All of our analyses were performed by PLINK v1.07 and 1.09 (v1.07 was only for haplotype-based analysis) (), Haploview v4.2 (), and R3.2.3 (https://www.r-project.org/). All the logistic regression models utilized an additive model (count of the minor allele for each SNP) and P-values of the t-test for logistic regression were two-tailed. We first performed a single SNP-based analysis using a logistic regression model including SNP, gender, age and trauma exposure. The interaction between SNP and trauma exposure was further included in the regression model. Then we carried out epistasis analysis to screen the 21 pairwise interactions formed by the seven SNPs with a simple logistic regression model, using the following formula: log(p/(1-p)) = SNP1+SNP2+SNP1×SNP2. The interaction P-value (Pinteraction) was calculated and subjected to Bonferroni correction for multiple comparisons. Afterwards, for the SNP pairs with Pcorrected < 0.05, we applied an initial logistic regression model: log(p/(1-p))=gender+age+SNP1+SNP2+SNP1× SNP2+trauma exposure+SNP1× trauma exposure+SNP2× trauma exposure+SNP1× SNP2 × trauma exposure. A following Akaike Information Criterion (AIC)-based model selection procedure was performed using a stepwise algorithm (, ) implemented in R to obtain the optimized logistic regression model. In our study, the final optimized model was log(p/(1-p))=gender+age+SNP1+SNP2+SNP1× SNP2+trauma exposure. The final model was applied to all the following logistic regression analyses. In addition, we further analyzed the gene–gene interactions in females and males respectively considering the important role of gender in PTSD genetic studies. […]

Pipeline specifications

Software tools PLINK, Haploview
Application GWAS
Chemicals Dopamine