As noted, not everyone in the sequenced sample of 1,706 individuals had psychophysiological data. The sequenced individuals who had psychophysiological data for any given endophenotype were a subset of the full 4,905 individuals with psychophysiology data included in the other articles of this special issue (see Figure 1 in Iacono et al., 2014). In addition to conducting association analyses in the sequenced individuals, we also attempted to utilize all available psychophysiological data from as many participants as possible. To do this, we imputed the 27 million sequenced variants into the full array genotyped sample. In imputation, one uses the more complete sequence information to fill in the many millions of variants that were not included on a particular genotype array. Imputation is well known to increase power for association and improve resolution of fine-mapping efforts to pinpoint likely causal variants (Howie, Fuchsberger, Stephens, Marchini, & Abecasis, 2012; Li, Willer, Ding, Scheet, & Abecasis, 2010).
