Polygenic Score (PGS) ID: PGS001331

Predicted Trait
Reported Trait Crohn's disease
Mapped Trait(s) Crohn's disease (EFO_0000384)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC322
Released in PGS Catalog: Oct. 21, 2021
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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_HC322
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 257
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: 50%
African: 25%
South Asian: 25%
4 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
—
[
  • 1,444 cases
  • , 268,260 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
PPM009142 PSS004442|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Crohns disease — AUROC: 0.65892 [0.54485, 0.77299] R²: 0.05502
Incremental AUROC (full-covars): -0.02526
PGS R2 (no covariates): 4e-05
PGS AUROC (no covariates): 0.49152 [0.37858, 0.60446]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009143 PSS004444|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Crohns disease — AUROC: 0.61269 [0.55802, 0.66736] R²: 0.01161
Incremental AUROC (full-covars): 0.02705
PGS R2 (no covariates): 0.00677
PGS AUROC (no covariates): 0.57919 [0.52051, 0.63786]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009144 PSS004445|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Crohns disease — AUROC: 0.71 [0.64649, 0.7735] R²: 0.03928
Incremental AUROC (full-covars): 0.01378
PGS R2 (no covariates): 0.00366
PGS AUROC (no covariates): 0.56349 [0.47905, 0.64793]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009145 PSS004446|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Crohns disease — AUROC: 0.56362 [0.53297, 0.59427] R²: 0.00529
Incremental AUROC (full-covars): 0.06267
PGS R2 (no covariates): 0.0063
PGS AUROC (no covariates): 0.57326 [0.54246, 0.60406]		 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
PSS004444 — —
[
  • 105 cases
  • , 24,800 controls
]
 — European non-white British ancestry UKB —
PSS004445 — —
[
  • 42 cases
  • , 7,789 controls
]
 — South Asian — UKB —
PSS004446 — —
[
  • 361 cases
  • , 67,064 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004442 — —
[
  • 20 cases
  • , 6,477 controls
]
 — African unspecified — UKB —