Table 6. Performance of the MRM and CART models for the prediction of α-thalassaemia genotype.
| Method | SNPID | Genotypes | Sensitivity % | Specificity % | PPV % | NPV% |
|---|---|---|---|---|---|---|
| (95%CI) | (95% CI) | (95% CI) | (95% CI) | |||
| MRM | rs2362744 | αα/αα | 64.8 (62.0-67.7) | 87.6 (86.1-89.1) | 75.9 (73.4-78.1) | 80.7 (79.3-81.9) |
| –α/αα | 82.5 (80.5-84.5) | 71.5 (69.2-73.8) | 73.1 (71.5-74.7) | 81.4 (79.4-83.1) | ||
| –α/–α | 84.8 (81.0-88.2) | 98.5 (97.9-98.9) | 90.1 (86.9-92.5) | 97.5 (96.9-98.0) | ||
| rs2854120 | αα/αα | 66.3 (63.5-69.1) | 89.6 (88.1-91.0) | 79.2 (76.8-81.5) | 81.6 (80.3-82.9) | |
| –α/αα | 85.7 (83.8-87.5) | 75.6 (73.4-77.8) | 76.7 (75.1-78.3) | 85.0 (83.2-86.5) | ||
| –α/–α | 95.1 (92.7-97.0) | 98.6 (98.2-99.1) | 92.3 (89.5-94.4) | 99.2 (98.8-99.5) | ||
| rs4021971 | αα/αα | 70.2 (67.4-72.9) | 87.3 (85.8-88.9) | 76.9 (74.6-79.1) | 83.1 (81.7-84.3) | |
| –α/αα | 82.2 (80.2-84.2) | 74.7 (72.5-77.0) | 75.4 (73.7-77.0) | 81.8 (80.0-83.5) | ||
| –α/–α | 81.4 (77.4-85.1) | 98.3 (97.8-98.8) | 89.0 (85.6-91.6) | 97.0 (96.3-97.5) | ||
| rs4021965 | αα/αα | 57.5 (54.5-60.5) | 86.9 (85.4-88.5) | 72.6 (69.9-75.0) | 77.4 (76.1-78.6) | |
| –α/αα | 80.0 (77.9-82.1) | 53.4 (50.9-56.0) | 61.7 (60.3-63.2) | 74.1 (71.9-76.2) | ||
| –α/–α | 58.2 (53.5-63.1) | 97.5 (96.8-98.1) | 71.6 (65.8-76.8) | 90.5 (89.9-91.2) | ||
| rs11639532 | αα/αα | 72.6 (69.9-75.2) | 88.6 (87.1-90.0) | 79.2 (77.0-81.3) | 84.4 (83.1-85.6) | |
| –α/αα | 82.9 (80.8-84.8) | 74.4 (72.2-76.6) | 75.3 (73.6-76.9) | 82.3 (80.5-83.9) | ||
| –α/–α | 85.9 (71.6-89.0) | 98.1 (97.5-98.6) | 86.8 (83.2-89.8) | 96.1 (95.4-96.7) | ||
| rs2858942 | αα/αα | 64.7 (61.8-67.5) | 88.2 (86.7-89.7) | 76.7 (74.2-79.0) | 80.7 (79.4-81.9) | |
| –α/αα | 80.0 (77.9-82.1) | 53.4 (50.9-56.0) | 61.7 (60.3-63.2) | 74.1 (71.9-76.2) | ||
| –α/–α | 81.0 (53.5-83.1) | 97.5 (96.8-98.1) | 71.6 (65.8-76.8) | 90.5 (89.9-91.2) | ||
| Combined | αα/αα | 66.0 (63.2-68.9) | 83.1 (81.4-84.9) | 70.1 (67.8-72.4) | 80.4 (79.0-81.7) | |
| –α/αα | 75.0 (72.7-77.3) | 72.3 (70.0-74.6) | 71.8 (70.0-73.5) | 75.5 (73.7-77.3) | ||
| –α/–α | 79.8 (75.6-83.6) | 96.6 (95.9-97.3) | 79.8 (76.1-83.1) | 96.7 (96.0-97.2) | ||
| CART | rs2362744 | αα/αα | 68.1 (53.8-83.7) | 97.7 (77.2-98.9) | 62.4 (59.8-64.7) | 75.9 (74.4-77.1) |
| –α/αα | 72.5 (70.2-74.9) | 68.4 (66.1-70.8) | 68.7 (66.8-70.3) | 72.6 (70.6-74.3) | ||
| –α/–α | 97.2 (88.9-97.4) | 99.1 (98.3-99.2) | 92.7 (90.0-94.7) | 98.8 (98.2-99.1) | ||
| rs2854120 | αα/αα | 76.5 (59.7-77.5) | 87.6 (85.0-88.2) | 73.9 (71.3-76.1) | 79.6 (78.2-80.7) | |
| –α/αα | 85.7 (79.7-83.8) | 72.9 (70.6-75.2) | 74.2 (72.3-75.6) | 81.0 (79.2-82.7) | ||
| –α/–α | 97.1 (92.6-97.6) | 98.5 (98.0-99.0) | 91.7 (88.7-93.8) | 99.2 (98.8-99.5) | ||
| rs4021971 | αα/αα | 78.8 (61.8-80.6) | 92.7 (90.4-94.0) | 82.6 (80.1-84.7) | 81.4 (80.0-82.5) | |
| –α/αα | 86.7 (84.9-88.4) | 76.6 (72.6-77.8) | 76.3 (74.6-77.8) | 85.7 (83.9-87.2) | ||
| –α/–α | 96.5 (92.6-97.0) | 97.5 (96.9-98.1) | 86.3 (83.2-89.0) | 99.3 (98.8-99.5) | ||
| rs4021965 | αα/αα | 69.0 (61.4-69.7) | 76.7 (74.7-78.7) | 62.4 (60.1-64.5) | 78.4 (76.7-79.6) | |
| –α/αα | 45.5 (36.7-56.4) | 61.3 (57.8-63.8) | 61.4 (59.5-63.0) | 65.9 (63.8-67.6) | ||
| –α/–α | 68.6 (64.1-69.1) | 96.7 (96.0-97.4) | 67.6 (62.1-72.6) | 91.0 (90.3-91.7) | ||
| rs11639532 | αα/αα | 75.0 (72.3-77.5) | 91.7 (90.4-92.9) | 84.4 (82.3-86.4) | 86.0 (84.7-87.2) | |
| –α/αα | 85.2 (83.3-87.1) | 81.6 (79.6-83.5) | 81.4 (79.7-83.0) | 85.6 (83.8-87.0) | ||
| –α/–α | 97.2 (90.3-98.4) | 96.7 (95.9-97.4) | 82.2 (78.9-85.1) | 98.9 (98.4-99.2) | ||
| rs2858942 | αα/αα | 60.8 (56.9-62.7) | 89.6 (88.2-91.0) | 77.7 (75.0-80.0) | 78.8 (77.6-80.0) | |
| –α/αα | 82.3 (80.3-84.3) | 69.3 (66.9-71.6) | 71.8 (70.0-73.2) | 80.7 (78.8-82.4) | ||
| –α/–α | 95.7 (87.6-96.4) | 96.9 (96.2-97.6) | 82.9 (79.5-85.8) | 98.5 (97.9-98.9) | ||
| Combined | αα/αα | 73.2 (70.6-75.9) | 80.1 (78.1-81.8) | 68.7 (66.6-70.8) | 83.3 (81.9-84.7) | |
| –α/αα | 73.6 (71.2-75.9) | 80.3 (78.1-82.1) | 77.7 (75.9-79.5) | 76.3 (74.7-77.9) | ||
| –α/–α | 93.2 (90.6-95.6) | 98.2 (98.3-99.2) | 92.9 (90.0-94.8) | 98.9 (98.5-99.3) |
Metrics were calculated for α-thalassaemia genotypes inferred from MRM and CART models created using 100 randomly selected individuals as a 'training' set, and repeated 1000 times. PPV = Positive predictive value; NPV= negative predictive value; MRM, Multiple-Regression Model; CART, Classification and Regression Trees.