the Jacobs method), 75%. Both estimates are considerably greater than the 25–50% reproducibility across methods estimated for several common CNV-calling algorithms19. All of the discordant mosaic detections appear to be due to false negatives. The Jacobs method is more conservative with respect to size threshold (2 Mb), while our method is more conservative with respect to sample quality (but calling mosaics involving segments less than 2 Mb when sample quality is sufficient). Therefore, the false negative rate of both methods appears to be high and the prevalence of clonal mosaic anomalies detected here is likely to be underestimated. Mosaic detection is difficult when the fraction of abnormal cells is extreme, when the anomaly length is small or when sample quality is low (i.e. high BAF/LRR variability).
