In the SAGE sample, CNVs with a frequency ≥ 1% were considered common, those with a frequency < 1% rare. Common BMI/obesity-associated CNVs were tested individually as well as in aggregate by count scores. The limited number of rare CNV variants expected to be detected in the SAGE sample made statistical analysis of individual rare CNVs inappropriate [45, 46]. Therefore, rare BMI/obesity-associated CNVs were tested by aggregate count scores (CNV-GRSSs). Additionally, since rare CNV burden scores have been associated with obesity [16, 19], the genome-wide load of rare CNVs was also tested by the count method. CNVs previously reported to be associated with BMI/obesity were considered the same region in the SAGE sample if the CNV boundaries shared at least 40% overlap with the CNV boundaries reported in the literature. Furthermore, since there is evidence that the positive predictive rate is increased for large CNVs, which is likely due to the increased number of probes in larger variants, common and rare scores were also constructed from CNVs ≥ 100-kb to potentially reduce the number of false positive calls in the score [38].
