Classification of clonal mosaic anomalies as duplication, deletion or aUPD was done using the median LRR and BAF deviations from non-anomalous segments (Figure 2b). Deviations from non-anomalous segments within the same sample were used to control for overall LRR variation among samples and for BAF asymmetry that occurs in some samples. Anomalies that are either terminal segments or whole chromosome and that have an LRR deviation within a ‘neutral zone’ (|LRR|<0.05) were classified as aUPD. This neutral zone was chosen because it includes nearly all of the wide splits (BAF deviation > 0.25) that have much smaller LRR deviations than expected for disomic/trisomic or disomic/monosomic transitions, while including very few interstitial anomalies (Supplementary Figure 3). All other anomalies (except for a few outliers) were classified as either duplications or deletions, depending on the sign of their LRR deviation. There is some ambiguity in classifying anomalies near the tip of the arrow, where the three transition zones intersect. This ambiguity is noted as ‘intensity.flag’ in Supplementary Table 3. Mixture proportions in mosaics can be estimated as position along the transitional line that connects the two constitutional states (Figure 2; see Supplementary Note).
