Table 1.
Performance of the VarCoPP on independent 10, 30, 100, and 300 random gene panels and on disease gene panels for the BBS and autism/ID genes, iterated 100 times on 100 random 1KGP individuals
| Gene panels | 10 Random genes | 30 Random genes | 100 Random genes | 300 Random genes | 21 BBS genes | 24 SFARI 1 genes | 79 SFARI 1 + 2 genes | 237 SFARI 1 + 2 + 3 genes | ||||||||
| Mean | SD | Mean | SD | Mean | SD | Mean | SD | Mean | SD | Mean | SD | Mean | SD | Mean | SD | |
| Combinations | 3.03 | 1.9 | 14.12 | 12.9 | 143.63 | 81.8 | 1,312 | 463.8 | 8.83 | 12.9 | 11.99 | 15.9 | 146.51 | 161.4 | 1,672.06 | 1,548.2 |
| % TNs, SS = 0 | 74.65 | 19.5 | 74.87 | 15.5 | 72.87 | 10.9 | 73.02 | 6.5 | 58.24 | 35.5 | 90.04 | 17.9 | 86.02 | 12.9 | 79.88 | 6.94 |
| % FPs | 7.23 | 11.6 | 6.54 | 8.9 | 7.93 | 6.8 | 7.39 | 3.4 | 12.66 | 20.4 | 1.99 | 7.4 | 2.81 | 5.0 | 4.22 | 3.2 |
| % 95-FPs | 4.62 | 8.9 | 4.48 | 7.8 | 5.53 | 5.4 | 5.13 | 2.7 | 8.45 | 16.2 | 1.39 | 4.9 | 2.02 | 4.1 | 2.75 | 2.4 |
| 95-FPs | 0.16 | 0.4 | 0.73 | 2.1 | 7.15 | 7.2 | 67.27 | 50.4 | 1.04 | 2.4 | 0.19 | 0.6 | 3.18 | 6.6 | 48.71 | 58.6 |
| % 99-FPs | 0.81 | 2.7 | 0.78 | 2.4 | 0.88 | 1.2 | 0.88 | 0.7 | 2.44 | 7.3 | 0.44 | 2.6 | 0.46 | 1.3 | 0.48 | 0.76 |
| 99-FPs | 0.03 | 0.1 | 0.11 | 0.4 | 1.16 | 1.5 | 11.86 | 11.5 | 0.35 | 0.9 | 0.03 | 0.2 | 0.67 | 1.9 | 7.80 | 11.7 |
95-FPs, FPs falling in the 95% confidence zone; 99-FPs, FPs falling in the 99% confidence zone; SFARI 1, high-confidence category; SFARI 2, strong candidate category; SFARI 3, suggestive evidence category.