(80% overlap). The mean of scores greater than zero was 95% for BAF- and 96% for LOH-detected anomalies (30% threshold), indicating that when an anomaly is detected in both scans, the breakpoints are highly reproducible. These reproducibility estimates are higher than the 40–60% that is typical for detecting CNVs using Hidden Markov Models (HMM)19,50, perhaps in large part because we do not attempt to detect small anomalies (the 5th percentile of anomalies we detect is 35 kb). In our experience, standard methods of CNV detection, such as PennCNV51, tend to break up large anomalies into many segments and to miss large mosaics.
