Instead, we assessed the quality of Canary-derived CNP genotypes by examining (i) inheritance in 91 independent parent-offspring trios and (ii) reproducibility across many laboratories. For the 1,177 diallelic CNPs tested (consisting of only a simple deletion or duplication, but not both), genotypes in 91 trios showed a mendelian inconsistency rate of approximately 0.005 per trio per CNP (Table 1). Copy number genotypes for 96 multiallelic CNPs6 were assessed for inheritance using Fisher’s h, which was distributed closely around 1.0, with only one CNP generating a P value <0.01. Canary genotypes were reproducible across the same HapMap samples run across seven independent labs, achieving an average sample call rate of 96.1% and a sample concordance with our reference dataset of 98.0%. Concordance with 783 independent copy number genotypes obtained by quantitative PCR (in 27 CNPs and 29 samples) averaged 97.6% across the seven labs. This is less complete and accurate than that for SNP genotypes, suggesting that further refinements are needed to either the algorithms or the underlying array data. Nonetheless, this performance across >1,000 CNPs far exceeds that of the small numbers (<100) of CNPs that have been genotyped in any previous study of appreciable sample size.
