Polygenic Score (PGS) ID: PGS001288

Predicted Trait
Reported Trait Inflammatory bowel disease
Mapped Trait(s) inflammatory bowel disease (EFO_0003767)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC95
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_HC95
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 195
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
—
[
  • 3,324 cases
  • , 266,380 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
PPM008938 PSS004741|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inflammatory bowel disease — AUROC: 0.64251 [0.54711, 0.73791] R²: 0.05914
Incremental AUROC (full-covars): 0.00245
PGS R2 (no covariates): 0.00027
PGS AUROC (no covariates): 0.52101 [0.42335, 0.61867]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008939 PSS004742|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inflammatory bowel disease — AUROC: 0.89429 [0.79091, 0.99767] R²: 0.2051
Incremental AUROC (full-covars): -0.0033
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.48687 [0.28135, 0.6924]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008940 PSS004743|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inflammatory bowel disease — AUROC: 0.63478 [0.60168, 0.66787] R²: 0.02287
Incremental AUROC (full-covars): 0.02492
PGS R2 (no covariates): 0.0102
PGS AUROC (no covariates): 0.58475 [0.55242, 0.61708]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008941 PSS004744|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inflammatory bowel disease — AUROC: 0.66934 [0.62525, 0.71343] R²: 0.03759
Incremental AUROC (full-covars): 0.004
PGS R2 (no covariates): 0.00311
PGS AUROC (no covariates): 0.55448 [0.50125, 0.6077]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008942 PSS004745|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inflammatory bowel disease — AUROC: 0.59461 [0.57544, 0.61378] R²: 0.01221
Incremental AUROC (full-covars): 0.06405
PGS R2 (no covariates): 0.01191
PGS AUROC (no covariates): 0.59586 [0.5768, 0.61492]		 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
PSS004741 — —
[
  • 36 cases
  • , 6,461 controls
]
 — African unspecified — UKB —
PSS004742 — —
[
  • 5 cases
  • , 1,699 controls
]
 — East Asian — UKB —
PSS004743 — —
[
  • 284 cases
  • , 24,621 controls
]
 — European non-white British ancestry UKB —
PSS004744 — —
[
  • 125 cases
  • , 7,706 controls
]
 — South Asian — UKB —
PSS004745 — —
[
  • 892 cases
  • , 66,533 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)