Polygenic Score (PGS) ID: PGS000940

Predicted Trait
Reported Trait Intestinal malabsorption (time-to-event)
Mapped Trait(s) Malabsorption (HP_0002024)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1132
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_HC1132
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 443
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
—
[
  • 2,295 cases
  • , 267,409 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
PPM007527 PSS004149|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE intestinal malabsorption — AUROC: 0.77831 [0.68833, 0.86829] R²: 0.08733
Incremental AUROC (full-covars): 0.1198
PGS R2 (no covariates): 0.02978
PGS AUROC (no covariates): 0.67977 [0.56558, 0.79395]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007528 PSS004150|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE intestinal malabsorption — AUROC: 0.77961 [0.74665, 0.81258] R²: 0.11095
Incremental AUROC (full-covars): 0.13283
PGS R2 (no covariates): 0.09823
PGS AUROC (no covariates): 0.76402 [0.72932, 0.79873]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007529 PSS004151|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE intestinal malabsorption — AUROC: 0.72065 [0.63105, 0.81026] R²: 0.05999
Incremental AUROC (full-covars): 0.05026
PGS R2 (no covariates): 0.04035
PGS AUROC (no covariates): 0.66531 [0.56469, 0.76593]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007530 PSS004152|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE intestinal malabsorption — AUROC: 0.75898 [0.73729, 0.78067] R²: 0.08993
Incremental AUROC (full-covars): 0.18915
PGS R2 (no covariates): 0.08413
PGS AUROC (no covariates): 0.75085 [0.7286, 0.77309]		 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
PSS004149 — —
[
  • 18 cases
  • , 6,479 controls
]
 — African unspecified — UKB —
PSS004150 — —
[
  • 208 cases
  • , 24,697 controls
]
 — European non-white British ancestry UKB —
PSS004151 — —
[
  • 38 cases
  • , 7,793 controls
]
 — South Asian — UKB —
PSS004152 — —
[
  • 553 cases
  • , 66,872 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)