Polygenic Score (PGS) ID: PGS001330

Predicted Trait
Reported Trait Crohn's disease [regional enteritis] (time-to-event)
Mapped Trait(s) Crohn's disease (EFO_0000384)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1101
Released in PGS Catalog: Oct. 21, 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_HC1101
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
—
[
  • 1,559 cases
  • , 268,145 controls
]
 European UKB — — — white British ancestry —

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
PPM009137 PSS004114|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.66243 [0.55234, 0.77252] R²: 0.05286
Incremental AUROC (full-covars): -0.02175
PGS R2 (no covariates): 0.00138
PGS AUROC (no covariates): 0.46272 [0.36718, 0.55826]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009138 PSS004115|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.86369 [0.7806, 0.94678] R²: 0.13339
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.14319
PGS AUROC (no covariates): 0.10664 [0.0, 0.28372]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009139 PSS004116|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.60269 [0.55209, 0.65328] R²: 0.01102
Incremental AUROC (full-covars): 0.02413
PGS R2 (no covariates): 0.00621
PGS AUROC (no covariates): 0.57593 [0.52318, 0.62867]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009140 PSS004117|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.69933 [0.63548, 0.76318] R²: 0.0344
Incremental AUROC (full-covars): 0.00201
PGS R2 (no covariates): 0.00147
PGS AUROC (no covariates): 0.53846 [0.46042, 0.6165]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009141 PSS004118|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE crohn's disease [regional enteritis] — AUROC: 0.55852 [0.52842, 0.58862] R²: 0.00474
Incremental AUROC (full-covars): 0.07412
PGS R2 (no covariates): 0.00669
PGS AUROC (no covariates): 0.5714 [0.54073, 0.60207]		 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
PSS004114 — —
[
  • 20 cases
  • , 6,477 controls
]
 — African unspecified — UKB —
PSS004115 — —
[
  • 2 cases
  • , 1,702 controls
]
 — East Asian — UKB —
PSS004116 — —
[
  • 117 cases
  • , 24,788 controls
]
 — European non-white British ancestry UKB —
PSS004117 — —
[
  • 48 cases
  • , 7,783 controls
]
 — South Asian — UKB —
PSS004118 — —
[
  • 393 cases
  • , 67,032 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)