The reproducibility of anomaly detection was assessed using samples genotyped in duplicate (N = 568 pairs). For each sample pair, we defined a unit of observation as a contiguous chromosomal region containing an anomaly in one or both samples. Each unit is given a score equal to the length of the intersection divided by the length of the union of anomalies in that unit. A reproducibility measure was defined as the fraction of units with a score greater than either 0.30 or 0.80 (chosen for comparison with published CNV studies). We also calculated the average of the scores that were greater than zero. Supplementary Table 2 summarizes these quantities for each study. For BAF, the mean reproducibility measure was 90% with a 30% overlap threshold and 82% with 80% overlap. For LOH, the means were 71% (30% overlap) and 67% (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
