The reproducibility (in 568 duplicate sample pairs) of all anomalies analyzed for mosaic status is 82% (with >80% overlap; see Methods and Supplementary Table 2 for details). For clonal mosaic anomalies in duplicate samples, the reproducibility is 15/22 = 68% and all discordant calls appear to be false negatives, based on examination of BAF/LRR plots. We also assessed the reproducibility of clonal mosaic anomaly calls in comparison with the results of Jacobs et al.18, who analyzed the same raw data for 5,510 subjects from the GENEVA Lung Cancer study. While both methods detected 83 mosaics, the GENEVA method described here detected an additional 28 mosaics (8 > 2 Mb) and the Jacobs method detected an additional 20 mosaics (all > 2 Mb). The overall reproducibility is 63% or, when considering only anomalies greater than 2 Mb (the size-detection limit of 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
