Table 2.
Exome-derived variables for the whole cohort and the training and validation cohorts.
| Variables | Whole Cohort N = 154 |
Training Cohort N = 101 |
Validation Cohort N = 53 |
p-Value | Adjusted p-Value |
|---|---|---|---|---|---|
| TMB status | 0.3 | >0.9 | |||
| Low | 134 (87%) | 90 (89%) | 44 (83%) | ||
| High | 20 (13%) | 11 (11%) | 9 (17%) | ||
| TMB score | 4.5 (2.8, 7.1) | 4.5 (3.1, 6.1) | 4.3 (2.6, 8.0) | >0.9 | >0.9 |
| MSI status | 0.4 | >0.9 | |||
| MSS | 146 (95%) | 97 (96%) | 49 (92%) | ||
| MSI | 8 (5.2%) | 4 (4.0%) | 4 (7.5%) | ||
| MSI score | 1.3 (1.0, 1.9) | 1.4 (1.0, 1.9) | 1.2 (0.9, 1.7) | 0.4 | >0.9 |
| TCR clonality | 7 (4, 12) | 7 (4, 12) | 7 (4, 10) | 0.5 | >0.9 |
| BCR clonality | 0.00 (0.00, 2.00) | 0.00 (0.00, 2.00) | 0.00 (0.00, 2.00) | >0.9 | >0.9 |
| NA | 2 | 2 | 0 | ||
| Neopeptides | 12 (7, 28) | 13 (6, 36) | 11 (7, 23) | 0.6 | >0.9 |
| NA | 3 | 2 | 1 | ||
| Strong neopeptides | 2.0 (1.0, 5.0) | 2.0 (1.0, 5.0) | 2.0 (1.0, 3.2) | 0.4 | >0.9 |
| NA | 3 | 2 | 1 | ||
| CNV signature 1 | 68 (53, 79) | 65 (51, 76) | 72 (61, 81) | 0.2 | >0.9 |
| Cut-off = 65.3%, 71.7% Low | 50 (50%) | 26 (50%) | >0.9 | >0.9 | |
| High | 50 (50%) | 26 (50%) | |||
| NA | 2 | 1 | 1 | ||
| CNV signature 2 | 0.00 (0.00, 0.00) | 0.00 (0.00, 0.00) | 0.00 (0.00, 0.00) | 0.4 | >0.9 |
| Cut-off = 0%, 0%, Low | 90 (90%) | 49 (94%) | 0.5 | >0.9 | |
| High | 10 (10%) | 3 (5.8%) | |||
| NA | 2 | 1 | 1 | ||
| CNV signature 3 | 13 (10, 19) | 13 (10, 19) | 13 (10, 20) | >0.9 | >0.9 |
| Cut-off = 13.2%, 13%, Low | 50 (50%) | 26 (50%) | >0.9 | >0.9 | |
| High | 50 (50%) | 26 (50%) | |||
| NA | 2 | 1 | 1 | ||
| CNV signature 4 | 0.00 (0.00, 0.00) | 0.00 (0.00, 0.00) | 0.00 (0.00, 0.00) | 0.7 | >0.9 |
| Cut-off = 0%, 0%, Low | 77 (77%) | 42 (81%) | 0.6 | >0.9 | |
| High | 23 (23%) | 10 (19%) | |||
| NA | 2 | 1 | 1 | ||
| CNV signature 5 | 11 (5, 18) | 0.12 (0.06, 0.19) | 10 (4, 16) | 0.12 | >0.9 |
| Cut-off = 11.8%, 9.8%, Low | 50 (50%) | 26 (50%) | >0.9 | >0.9 | |
| High | 50 (50%) | 26 (50%) | |||
| NA | 2 | 1 | 1 | ||
| CNV signature 6 | 0.00 (0.00, 0.00) | 0.00 (0.00, 0.00) | 0.00 (0.00, 0.00) | >0.9 | >0.9 |
| Cut-off = 0%, 0%, Low | 88 (88%) | 46 (88%) | >0.9 | >0.9 | |
| High | 12 (12%) | 6 (12%) | |||
| NA | 2 | 1 | 1 | ||
| CNV signature 7 | 0.00 (0.00, 0.08) | 0.00 (0.00, 11) | 0.00 (0.00, 4) | 0.2 | >0.9 |
| Cut-off = 0%, 0%, Low | 55 (56%) | 34 (65%) | 0.2 | >0.9 | |
| High | 44 (44%) | 18 (35%) | |||
| NA | 3 | 2 | 1 | ||
| TCR Pielou’s score | 0.98 (0.96, 1.00) | 0.99 (0.96, 1.00) | 0.97 (0.95, 1.00) | 0.3 | >0.9 |
| NA | 10 | 6 | 4 | ||
| BCR Pielou’s score | 1.00 (0.72, 1.00) | 0.99 (0.00, 1.00) | 1.00 (0.96, 1.00) | 0.078 | >0.9 |
| NA | 84 | 55 | 29 | ||
| TCR Shannon entropy | 2.81 (2.00, 3.54) | 2.85 (2.00, 3.55) | 2.75 (2.00, 3.32) | 0.6 | >0.9 |
| NA | 10 | 6 | 4 | ||
| BCR Shannon entropy | 1.44 (0.72, 2.00) | 1.26 (0.00, 2.30) | 1.48 (1.00, 2.00) | 0.7 | >0.9 |
| NA | 84 | 55 | 29 | ||
| KRAS | 0.7 | >0.9 | |||
| WT | 136 (88%) | 90 (89%) | 46 (87%) | ||
| Mutated | 18 (12%) | 11 (11%) | 7 (13%) | ||
| STK11 | 0.7 | >0.9 | |||
| WT | 146 (95%) | 95 (94%) | 51 (96%) | ||
| Mutated | 8 (5.2%) | 6 (5.9%) | 2 (3.8%) | ||
| APC | >0.9 | >0.9 | |||
| WT | 147 (95%) | 96 (95%) | 51 (96%) | ||
| Mutated | 7 (4.5%) | 5 (5.0%) | 2 (3.8%) | ||
| RNF43 | 0.4 | >0.9 | |||
| WT | 148 (96%) | 98 (97%) | 50 (94%) | ||
| Mutated | 6 (3.9%) | 3 (3.0%) | 3 (5.7%) | ||
| CD274 | 0.5 | >0.9 | |||
| Amplification | 9 (5.8%) | 5 (5.0%) | 4 (7.5%) | ||
| No amplification | 145 (94%) | 96 (95%) | 49 (92%) |
Continuous variables are described by median values and interquartile range (IQR). Categorical variables were described by number of observation and percentages (%). TMB: Tumor Mutational Burden; MSI: Microsatellite Instability; MSS: Microsatellite Stable; TCR: T-Cell Receptor; BCR: B-Cell Receptor; CNV: Copy Number Variant.