Polygenic Score (PGS) ID: PGS001390

Predicted Trait
Reported Trait Duodenal ulcer (time-to-event)
Mapped Trait(s) duodenal ulcer (EFO_0004607)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1084
Released in PGS Catalog: Nov. 25, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC1084
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 220
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 4,560 cases
  • , 265,144 controls
]
 European UKB — — — white British ancestry Training + validation cohort (train_val)

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM005200 PSS004094|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.71018 [0.66062, 0.75975] R²: 0.05605
Incremental AUROC (full-covars): 0.00294
PGS R2 (no covariates): 0.00399
PGS AUROC (no covariates): 0.5623 [0.50635, 0.61825]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005201 PSS004095|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.66565 [0.55325, 0.77805] R²: 0.04606
Incremental AUROC (full-covars): 0.00253
PGS R2 (no covariates): 0.006
PGS AUROC (no covariates): 0.56376 [0.43513, 0.6924]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005202 PSS004096|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.71045 [0.68829, 0.73261] R²: 0.06289
Incremental AUROC (full-covars): 0.0043
PGS R2 (no covariates): 0.0047
PGS AUROC (no covariates): 0.55991 [0.53425, 0.58556]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005203 PSS004097|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.70619 [0.66443, 0.74795] R²: 0.0567
Incremental AUROC (full-covars): 0.00581
PGS R2 (no covariates): 0.00168
PGS AUROC (no covariates): 0.54031 [0.491, 0.58961]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005204 PSS004098|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.68746 [0.67261, 0.70231] R²: 0.04811
Incremental AUROC (full-covars): 0.00644
PGS R2 (no covariates): 0.00484
PGS AUROC (no covariates): 0.56101 [0.54453, 0.5775]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS004094 — —
[
  • 95 cases
  • , 6,402 controls
]
 — African unspecified — UKB —
PSS004095 — —
[
  • 24 cases
  • , 1,680 controls
]
 — East Asian — UKB —
PSS004096 — —
[
  • 481 cases
  • , 24,424 controls
]
 — European non-white British ancestry UKB —
PSS004097 — —
[
  • 135 cases
  • , 7,696 controls
]
 — South Asian — UKB —
PSS004098 — —
[
  • 1,164 cases
  • , 66,261 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)