TABLE 3b.
MGI PheRS estimate and diagnostics using beta estimates from MGI
| Time threshold (in years prior to diagnosis) |
||||
|---|---|---|---|---|
| 0 years | 1 year | 2 years | 5 years | |
| Odds Ratio | 7.86 | 3.69 | 3.71 | 5.54 |
| Odds Ratio 95% CI | (6.22, 10.13) | (2.73, 5.22) | (2.69, 5.33) | (3.37, 10.46) |
| P-value | 4.91E-62 | 2.61E-15 | 5.33E-14 | 1.65E-09 |
| AUC | 0.853 | 0.711 | 0.702 | 0.694 |
| AUC 95% CI | 0.829, 0.877 | 0.673, 0.749 | 0.660, 0.743 | 0.652, 0.736 |
| HL Stat, P-value | 6.30, 6.14e-01 | 0.54, 1.00e+00 | 1.57, 9.91e-01 | 0.52, 1.00e+00 |
| Brier score | 0.11420 | 0.18076 | 0.18506 | 0.17231 |
| Top %-ile OR (95% CI) | ||||
| 1st percentile | 23.86 (20.22, 28.84) | 14.14 (7.02, 48.17) | 10.36 (5.64, 14.62) | 26.96 (10.44, 104.47) |
| 2nd percentile | 23.86 (20.22, 28.84) | 10.08 (6.19, 23.41) | 9.16 (5.12, 27.90) | 17.77 (8.06, 45.88) |
| 5th percentile | 33.53 (23.19, 49.45) | 6.50 (4.34, 12.91) | 7.17 (4.20, 13.22) | 11.28 (2.92, 101.50) |
| 10th percentile | 21.88 (5.87, 194.23) | 4.06 (2.81, 9.97) | 4.58 (2.74, 8.50) | 11.28 (2.92, 101.50) |
| 25th percentile | 21.88 (5.87, 194.23) | 4.06 (2.81, 9.97) | 4.58 (2.74, 8.50) | 11.28 (2.92, 101.50) |
Abbreviations: CI, confidence interval; OR, odds ratio; HL, Hosmer-Lemeshow Goodness of Fit test; %-ile, percentile; PheRS, phenotype risk score
Notes:
- The estimates and diagnostic values in this table correspond to pancreatic cancer PheRS constructed in MGI using association estimates obtained from time-restricted co-occurrence analysis in the matched MGI discovery cohort.
- The odds ratio, corresponding 95% confidence interval estimate, and p-value come from a logistic GLM model for the PheRS on pancreatic cancer, adjusted for, sex, birthyear, genotyping array, and the first four principal components of the genotype data.
- The AUC and corresponding 95% confidence interval are from an unadjusted ROC model.
- The Hosmer-Lemeshow test statistic and p-value and the Brier score are from a matched, unadjusted logistic GLM model for pancreatic cancer case/control status.
- The percentile-based odds ratios and confidence intervals come from a Firth-corrected logistic regression model on pancreatic cancer case/control status adjusted for sex, age at time threshold, genotyping array, and the first four principal components of the genotype data.