size threshold was set to detect only clonal mosaic events greater than 2 Mbps to minimize the false discovery of constitutional copy number variants. Copy-neutral LOH and copy-loss events could be detected for mosaic proportions between 7% and 95% (Figure 1) with sensitivity that was affected by the signal-to-noise ratio characteristic of each microarray assay and sample quality. There was reduced sensitivity to distinguish between copy-neutral LOH and copy-loss events for mosaic proportions less than 15% across the autosomes. The magnitude of BAF differences for single-copy gain events was 1/3 of the magnitude of copy-neutral LOH or copy-loss events, reducing the sensitivity for calling copy-gain events. As a result, single copy gain events could only be reliably detected for mosaic proportions between 22% and 88%, with ambiguity in distinguishing copy-gain from copy-neutral LOH for mosaic proportions of less than 20%. Since DNA was obtained for the purpose of performing a GWAS, it was not possible to further explore the developmental and clonal characteristics of mosaic events detected in these individuals (e.g. by studying DNA from fractionated blood and other tissue types, determining cell composition of buccal samples, or effect of DNA collection and extraction methods on detection and accuracy of
