Polygenic Score (PGS) ID: PGS001516

Predicted Trait
Reported Trait Other diseases of intestine (time-to-event)
Mapped Trait(s) intestinal disease (EFO_0009431)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1112
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_HC1112
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 90
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
—
[
  • 13,147 cases
  • , 256,557 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
PPM005210 PSS004129|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of intestine — AUROC: 0.71458 [0.68087, 0.7483] R²: 0.07935
Incremental AUROC (full-covars): 0.00184
PGS R2 (no covariates): 0.00206
PGS AUROC (no covariates): 0.53644 [0.50022, 0.57266]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005211 PSS004130|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of intestine — AUROC: 0.71022 [0.64099, 0.77946] R²: 0.09409
Incremental AUROC (full-covars): 0.00324
PGS R2 (no covariates): 0.00207
PGS AUROC (no covariates): 0.53358 [0.4606, 0.60656]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005212 PSS004131|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of intestine — AUROC: 0.65457 [0.63994, 0.6692] R²: 0.04465
Incremental AUROC (full-covars): 0.00302
PGS R2 (no covariates): 0.00297
PGS AUROC (no covariates): 0.54106 [0.52507, 0.55705]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005213 PSS004132|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of intestine — AUROC: 0.70984 [0.68398, 0.7357] R²: 0.07373
Incremental AUROC (full-covars): -0.001
PGS R2 (no covariates): 0.00026
PGS AUROC (no covariates): 0.48728 [0.45689, 0.51767]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005214 PSS004133|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of intestine — AUROC: 0.62222 [0.6128, 0.63164] R²: 0.02673
Incremental AUROC (full-covars): 0.00391
PGS R2 (no covariates): 0.0026
PGS AUROC (no covariates): 0.53789 [0.5278, 0.54798]		 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
PSS004129 — —
[
  • 235 cases
  • , 6,262 controls
]
 — African unspecified — UKB —
PSS004130 — —
[
  • 54 cases
  • , 1,650 controls
]
 — East Asian — UKB —
PSS004131 — —
[
  • 1,301 cases
  • , 23,604 controls
]
 — European non-white British ancestry UKB —
PSS004132 — —
[
  • 333 cases
  • , 7,498 controls
]
 — South Asian — UKB —
PSS004133 — —
[
  • 3,290 cases
  • , 64,135 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)