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Chunk #21 — SAMPLE & METHODS — Functional Analyses

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A genome wide association study of fast beta EEG in families of European ancestry.
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We utilized publicly available data from the UK Brain Expression Consortium (BRAINEAC; http://www.braineac.org/) to examine whether the most significant GWAS variant for fast beta EEG was an expression quantitative trait locus (eQTL) for any known gene. BRAINEAC draws on data from 134 neuropathologically normal individuals of EA and assesses 10 different regions of the brain, including: cerebellar cortex, frontal cortex, hippocampus, medulla (inferior olivary nucleus), occipital cortex (primary visual cortex), putamen, substantia nigra, thalamus, temporal cortex, and intralobular white matter (Trabzuni et al., 2011). All p-values presented are Bonferonni corrected for multiple-testing, based on the ten brain regions examined. Due to the large number of brain regions examined, only the SNPs genome-wide associated with fast beta EEG were examined in BRAINEAC to minimize multiple-testing. All associations that withstood multiple testing were examined in the Genotype-Tissue Expression Project (GTex) database (www.gtexportal.org) to confirm eQTL findings (For brain eQTLs, sample sizes ranged from 70–127). GeneMANIA Cytoscape 3.0.0 plugin (Mostafavi et al., 2008), a multiple association network integration algorithm for predicting gene function, was employed to identify genes in related gene networks; physical,