cytogenetic or molecular validation was not performed, neither method detected notable false-positive events based on manual review of the data. The concordance rate is 75% if considering events > 2 Mb (the cut-off for this analysis) or 63% if considering all events, both of which are considerably better than the 25-50% concordance rates observed across CNV detection methods29-31. Our method is more conservative in the size of events detected, while the GENEVA method is more conservative with respect to sample quality, but provides calls for smaller events when assay quality is sufficient. Better approaches are needed to characterize smaller size events accurately as either mosaic or constitutional and to estimate their frequency. Further improvements to data normalization, segmentation and event classification methods will also likely reduce false-negative rates.
