For the initial Fisher’s exact test, related individuals were not controlled for, as our primary objective was to detect CNVs in multiple samples regardless of relatedness. CNVRs passing this initial screen were scored for statistical significance based on a permuted P value, which permutes case and control labels randomly for all samples, with the condition that related individuals have same label. Based on the number of samples with the CNVR being calculated in randomly assigned ‘cases’ and ‘controls’, a Fisher’s exact test P value was assigned. The number of hypothetical scenarios with significance equal or greater to this P value provides the permuted P value, which corrects for relatedness. The Fisher’s exact test P value and the counts of cases and controls with each CNVR are provided in Table 1 for transparency.
