TABLE 3a.
UKB 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 | 1.66 | 1.51 | 1.57 | 1.56 |
| Odds Ratio 95% CI | (1.62, 1.70) | (1.48, 1.55) | (1.51, 1.63) | (1.50, 1.62) |
| P-value | 0.00E+00 | 1.61E-245 | 1.48E-111 | 1.31E-108 |
| AUC | 0.699 | 0.657 | 0.606 | 0.603 |
| AUC 95% CI | 0.679, 0.719 | 0.635, 0.679 | 0.583, 0.629 | 0.583, 0.623 |
| HL Stat, P-value | 45.44, 3.04e-07 | 89.75, 5.55e-16 | 100.72, 0.00e+00 | 38.71, 5.56e-06 |
| Brier score | 0.00168 | 0.00168 | 0.00167 | 0.00167 |
| Top %-ile OR (95% CI) | ||||
| 1st percentile | 15.77 (14.51, 20.05) | 21.24 (19.47, 27.44) | 14.07 (12.70, 17.93) | 1.75 (1.19, 2.58) |
| 2nd percentile | 20.14 (18.84, 25.67) | 12.20 (11.40, 15.93) | 9.60 (8.78, 12.23) | 10.20 (9.34, 12.99) |
| 5th percentile | 1.28 (0.90, 1.88) | 0.71 (0.55, 0.89) | 0.77 (0.63, 0.90) | 0.62 (0.47, 0.77) |
| 10th percentile | 1.28 (0.90, 1.88) | 0.71 (0.55, 0.89) | 0.77 (0.63, 0.90) | 0.62 (0.47, 0.77) |
| 25th percentile | 1.28 (0.90, 1.88) | 0.71 (0.55, 0.89) | 0.77 (0.63, 0.90) | 0.62 (0.47, 0.77) |
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 UKB 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 for pancreatic cancer case/control status.
- 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, birthyear, genotyping array, and the first four principal components of the genotype data.