Clonal mosaic anomalies were identified in GENEVA family studies by using transmitted anomalies to characterize the bivariate BAF/LRR distribution expected for non-mosaic (constitutional) anomalies. For transmitted anomalies, this distribution is approximately bivariate normal within a study and we used this distribution to estimate a 95% prediction ellipse52, which defines an area likely to contain most of the constitutional anomalies (Supplementary Figure 13). Among the anomalies used to identify mosaics, the majority are 3N duplications. There is also a small cluster of 4N anomalies, but we did not attempt to detect 3N/4N mosaics. Anomalies outside of these two clusters contain mosaics and artifacts. The latter consist of false positives and anomalies with inaccurate breakpoints (which distorts the median BAF/LRR values). To distinguish between the mosaics and artifacts, we performed a manual review of BAF/LRR plots for all anomalies that fell outside of the 95% prediction ellipse and below the mean LRR for anomalies used to define the ellipse. The non-family studies were analyzed in a similar way, except that we replaced the class of transmitted anomalies with polymorphic CNVs. The latter
