The accuracy of our software methods to detect clonal mosaic abnormalities was previously addressed and we were able to validate 100% of 42 events in 34 individuals from the Spanish Bladder Cancer Study using confirmatory cytogenetic assays16 (Supplementary Figure 3). We have also performed a comparison of mosaic events in samples from the EAGLE and PLCO lung cancer studies which were independently analyzed as part of the Gene, Environment Association studies consortium (GENEVA) report on mosaic events28. A total of 83 mosaic events in individuals from the EAGLE and PLCO lung cancer studies were detected in common, 20 additional events of size less than 2 Mb and 8 events greater than 2 Mb were detected by GENEVA and not by our study, while we detected 20 additional events (size > 2 Mb) that were not detected by GENEVA. Although additional cytogenetic or molecular validation was not performed, neither method detected notable false-positive events based on manual review of the data. The concordance rate is 75% if considering events > 2 Mb (the cut-off for this analysis) or 63% if considering
