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Chunk #9 — Materials and Methods — Data summarization and dimension reduction

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Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
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Amphetamine treatment significantly affected most of the phenotypes (Table S2). Exploratory data analyses of each phenotype using both individual data and the mean values showed the expected drug effects across the entire sample (Figure 1A), but we observed substantial variability at individual data points (Figure 1B). Average phenotypic values obtained at baseline, before the drug was administered (0 min), were similar across the three sessions. Average phenotypic values obtained at the second time point (30 min) typically showed minor drug effects, whereas phenotypic values at each of the remaining time points changed in a dose-dependent manner. Although the mean values at the last four time points were generally consistent with the expected time course (increasing to a peak, and then slowly decreasing) these time-points were highly correlated (Figure 1C) and the differences among these means were generally small compared with the difference from the mean at the 0 time point, particularly in the non-placebo sessions. Therefore, we summarized the six measurements for each phenotype in each session, for each individual, using two numbers: (i) the first time point (0 min),