Before examining the parent-child transmission of CNVs in trios, we first confirmed parentage of all trios included in CNV analysis. We used genotypes from 486 CNPs (see Supplemental Experimental Procedures) to test relatedness. For each pair within a trio (i.e., mother-child, father-child, and mother-father), genetic relatedness was tested by the Glaubitz Relationship Score (GRS) (Glaubitz et al., 2003). Based on this test, first-degree relative pairs (i.e., mother-child and father-child) were clearly distinguishable from the distribution of GRS scores for unrelated individuals (i.e., mother-father pairs) as shown in Figure S2. We applied a threshold of > 0.37 to define relatedness. Thirty-two families failed parentage testing, and the remaining 788 trios were included in our analysis. Pairwise relationship of all subjects in 788 trios was confirmed using a second relatedness testing method, Graphical Representation of Relationships (GRR, http://www.sph.umich.edu/csg/abecasis/GRR/).
