“…Among the advantages of calling CNVs from WES data, characterization of complex genotypes comprising both CNVs and SNVs or small insertions/deletions minimizes costs and time to final diagnosis [38][39][40], while also allowing differentiation between true or false homozygosity, as well as compound heterozygosity of variants in AR genes. In point of fact, 11 patients with pathogenic SNVs in AR genes were falsely characterized as either homozygous for an SNV (patients 14, 25, 30, and 40), when they actually carried a large deletion in-trans configuration with the SNV (Table 3; Supplementary Materials, Table S3), or as carriers (patients 8, 10, 20, 21, 23, 29, and 32), while they really were compound heterozygotes for the SNV and a CNV in the same AR gene (Table 3; Supplementary Materials, Table S3).…”