Table 1 Confirmation of CNV benchmark sets by three orthogonal methods (based on regions, Mb)
Confidence level | Collapsed calls from NGS | Affymetrix Cytoscan | Illumina array | Bionano | Validated by at least one technology | Validated by at least two technologies |
|---|---|---|---|---|---|---|
Copy number gain | ||||||
 Strong | 1542.1 | 858.2 | 883.3 | 1243.8 | 1357.2 (88.0%) | 1099.5 (72.3%) |
 Medium | 35.0 | 3.1 | 0.3 | 11.7 | 14.6 (41.8%) | 0.5 (1.3%) |
 Weak | 69.1 | 0.1 | 0.1 | 12.9 | 13.0 (18.8%) | 0.1 (0.1%) |
 Neutral | 992.3 | 0.7 | 0.3 | 17.3 | 18.1 (1.8%) | 0.2 (0.0%) |
Copy number loss | ||||||
 Strong | 79.7 | 79.7 | 79.5 | 78.9 | 79.7 (100%) | 79.6 (99.9%) |
 Medium | 1.1 | 1.1 | 0.5 | 0.3 | 1.1 (94.9%) | 0.5 (44.1%) |
 Weak | 24.2 | 23.3 | 7.6 | 7.7 | 23.3 (96.1%) | 7.7 (31.8%) |
 Neutral | 1518.9 | 799.8 | 23.5 | 24.4 | 800.7 (52.7%) | 24.5 (1.6%) |