Polygenic Score (PGS) ID: PGS000943

Predicted Trait
Reported Trait Cholecystitis (time-to-event)
Mapped Trait(s) Cholecystitis (HP_0001082)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1126
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC1126
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 5
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
—
[
  • 2,799 cases
  • , 266,905 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
PPM007541 PSS004144|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.73752 [0.65767, 0.81736] R²: 0.06767
Incremental AUROC (full-covars): 0.00596
PGS R2 (no covariates): 0.00524
PGS AUROC (no covariates): 0.59329 [0.50586, 0.68073]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007542 PSS004145|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.8085 [0.69534, 0.92165] R²: 0.14928
Incremental AUROC (full-covars): -0.00085
PGS R2 (no covariates): 0.00478
PGS AUROC (no covariates): 0.41038 [0.27687, 0.54388]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007543 PSS004146|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.63478 [0.60059, 0.66896] R²: 0.02044
Incremental AUROC (full-covars): 0.00654
PGS R2 (no covariates): 0.00332
PGS AUROC (no covariates): 0.52696 [0.48804, 0.56587]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007544 PSS004147|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.64056 [0.57812, 0.70301] R²: 0.02887
Incremental AUROC (full-covars): 0.01113
PGS R2 (no covariates): 0.00762
PGS AUROC (no covariates): 0.56004 [0.4865, 0.63358]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007545 PSS004148|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.59655 [0.57661, 0.6165] R²: 0.01081
Incremental AUROC (full-covars): 0.00936
PGS R2 (no covariates): 0.00239
PGS AUROC (no covariates): 0.53954 [0.51772, 0.56136]		 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
PSS004144 — —
[
  • 35 cases
  • , 6,462 controls
]
 — African unspecified — UKB —
PSS004145 — —
[
  • 14 cases
  • , 1,690 controls
]
 — East Asian — UKB —
PSS004146 — —
[
  • 233 cases
  • , 24,672 controls
]
 — European non-white British ancestry UKB —
PSS004147 — —
[
  • 66 cases
  • , 7,765 controls
]
 — South Asian — UKB —
PSS004148 — —
[
  • 706 cases
  • , 66,719 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)