For continuous variables each stratum of a “case” proband matched to 5 “control” probands was treated as a block and the data analyzed as a randomized block design by using analysis of covariance. Thus mean values were allowed to vary across blocks and to be altered by case-control status. The difference due to the presence of the CNV of interest was assessed with an F-test with N, M degrees-of-freedom (N is the number of CNVs of interest and M is the residual degrees-of-freedom after accounting for model terms). Because IQ is known to affect many behavioral measures associated with ASD, it was treated as a covariate in models for outcomes besides itself and Body Mass Index (BMI). For diagnostic status, matching was taken into account by using a conditional logit model.
