Polygenic Score (PGS) ID: PGS001256

Predicted Trait
Reported Trait Gallstones
Mapped Trait(s) gallstones (EFO_0004210)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC188
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_HC188
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 876
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
—
[
  • 13,557 cases
  • , 256,147 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
PPM008785 PSS004334|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.68692 [0.64329, 0.73056] R²: 0.04974
Incremental AUROC (full-covars): 0.02029
PGS R2 (no covariates): 0.00785
PGS AUROC (no covariates): 0.56814 [0.51821, 0.61807]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008786 PSS004335|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.67793 [0.60585, 0.75001] R²: 0.06195
Incremental AUROC (full-covars): 0.00834
PGS R2 (no covariates): 0.00064
PGS AUROC (no covariates): 0.52583 [0.44852, 0.60314]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008787 PSS004336|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.66809 [0.65163, 0.68454] R²: 0.05165
Incremental AUROC (full-covars): 0.04397
PGS R2 (no covariates): 0.0275
PGS AUROC (no covariates): 0.62496 [0.60759, 0.64234]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008788 PSS004337|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.68743 [0.65645, 0.71841] R²: 0.0581
Incremental AUROC (full-covars): 0.01295
PGS R2 (no covariates): 0.00775
PGS AUROC (no covariates): 0.56733 [0.53369, 0.60096]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008789 PSS004338|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.67227 [0.66315, 0.68138] R²: 0.05484
Incremental AUROC (full-covars): 0.04156
PGS R2 (no covariates): 0.02494
PGS AUROC (no covariates): 0.6171 [0.6073, 0.6269]		 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
PSS004334 — —
[
  • 136 cases
  • , 6,361 controls
]
 — African unspecified — UKB —
PSS004335 — —
[
  • 55 cases
  • , 1,649 controls
]
 — East Asian — UKB —
PSS004336 — —
[
  • 1,055 cases
  • , 23,850 controls
]
 — European non-white British ancestry UKB —
PSS004337 — —
[
  • 278 cases
  • , 7,553 controls
]
 — South Asian — UKB —
PSS004338 — —
[
  • 3,344 cases
  • , 64,081 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)