Polygenic Score (PGS) ID: PGS001301

Predicted Trait
Reported Trait Malabsorption/coeliac disease
Mapped Trait(s) celiac disease (EFO_0001060)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC303
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_HC303
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 428
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
—
[
  • 1,848 cases
  • , 267,856 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
PPM009001 PSS004423|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malabsorption/coeliac disease — AUROC: 0.84259 [0.73437, 0.95081] R²: 0.12308
Incremental AUROC (full-covars): 0.02463
PGS R2 (no covariates): 0.03018
PGS AUROC (no covariates): 0.68151 [0.48835, 0.87467]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009002 PSS004424|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malabsorption/coeliac disease — AUROC: 0.81472 [0.7798, 0.84965] R²: 0.15108
Incremental AUROC (full-covars): 0.1791
PGS R2 (no covariates): 0.14221
PGS AUROC (no covariates): 0.80994 [0.77441, 0.84547]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009003 PSS004425|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malabsorption/coeliac disease — AUROC: 0.81699 [0.73267, 0.9013] R²: 0.11397
Incremental AUROC (full-covars): 0.06035
PGS R2 (no covariates): 0.07098
PGS AUROC (no covariates): 0.76239 [0.65258, 0.87221]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009004 PSS004426|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malabsorption/coeliac disease — AUROC: 0.83351 [0.81372, 0.85329] R²: 0.14905
Incremental AUROC (full-covars): 0.25775
PGS R2 (no covariates): 0.14224
PGS AUROC (no covariates): 0.82867 [0.80826, 0.84908]		 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
PSS004423 — —
[
  • 7 cases
  • , 6,490 controls
]
 — African unspecified — UKB —
PSS004424 — —
[
  • 178 cases
  • , 24,727 controls
]
 — European non-white British ancestry UKB —
PSS004425 — —
[
  • 24 cases
  • , 7,807 controls
]
 — South Asian — UKB —
PSS004426 — —
[
  • 451 cases
  • , 66,974 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)