Computational protocol: Polymorphisms in melatonin synthesis pathways: possible influences on depression

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Protocol publication

[…] The associations of ASMT SNPs with either the QIDS-SR or GDS depression scales were computed with PLINK [], using linear regression in an additive model, controlling for age, gender (when applicable), and clinic site (when applicable). To control for ancestry background, we performed a multidimensional scaling analysis (MDS) with the AIMs and used two ancestry-informative marker dimensions as covariates in the association analyses. Because we were seeking to replicate the previous reports of Galecki et al. [] and Soria et al. [] of SNPs associated with depression, a significance criterion of P = 0.05 was chosen for ASMT rs4446909 and AANAT rs8150. R2 represented the percentage of depression variance predicted by the SNP, excluding covariates from the model. For rs4446909, a recessive model was also considered, but it did not improve the evidence for association of the SNP with depression. Association of ASMT and AANAT SNPs with BALM was examined in the UCSD and Sleep Center participants with a dominant model, using similar linear regressions controlled for age, gender, and MDS factors, and correcting for multiple testing of 610 SNPs. The dominant model was selected because of evidence that morningness-eveningness is inherited as a dominant trait []. Among the bipolar patients, the associations of ASMT rs4446909 and NTRK2 rs1387923 with lithium response and Alda scale response were assessed with SPSS, using the general linear model and backwards stepwise logistic regression, controlling for age and gender. […]

Pipeline specifications

Software tools PLINK, SPSS
Applications Miscellaneous, GWAS
Organisms Homo sapiens
Chemicals Lithium, Melatonin