Polygenic Score (PGS) ID: PGS000942

Predicted Trait
Reported Trait Cholecystitis
Mapped Trait(s) Cholecystitis (HP_0001082)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC225
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_HC225
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 391
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
—
[
  • 12,012 cases
  • , 257,692 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
PPM007536 PSS004364|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.68703 [0.64283, 0.73122] R²: 0.05062
Incremental AUROC (full-covars): 0.01542
PGS R2 (no covariates): 0.00638
PGS AUROC (no covariates): 0.57182 [0.52186, 0.62177]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007537 PSS004365|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.68844 [0.61497, 0.76192] R²: 0.06303
Incremental AUROC (full-covars): 0.01478
PGS R2 (no covariates): 0.00267
PGS AUROC (no covariates): 0.53743 [0.45172, 0.62313]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007538 PSS004366|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.64946 [0.63161, 0.6673] R²: 0.03849
Incremental AUROC (full-covars): 0.03425
PGS R2 (no covariates): 0.01921
PGS AUROC (no covariates): 0.60901 [0.59053, 0.6275]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007539 PSS004367|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.65729 [0.62309, 0.69148] R²: 0.04114
Incremental AUROC (full-covars): 0.01289
PGS R2 (no covariates): 0.00646
PGS AUROC (no covariates): 0.56972 [0.5349, 0.60453]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007540 PSS004368|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.64339 [0.63352, 0.65325] R²: 0.03651
Incremental AUROC (full-covars): 0.03273
PGS R2 (no covariates): 0.01602
PGS AUROC (no covariates): 0.59436 [0.5838, 0.60493]		 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
PSS004364 — —
[
  • 128 cases
  • , 6,369 controls
]
 — African unspecified — UKB —
PSS004365 — —
[
  • 48 cases
  • , 1,656 controls
]
 — East Asian — UKB —
PSS004366 — —
[
  • 926 cases
  • , 23,979 controls
]
 — European non-white British ancestry UKB —
PSS004367 — —
[
  • 256 cases
  • , 7,575 controls
]
 — South Asian — UKB —
PSS004368 — —
[
  • 2,978 cases
  • , 64,447 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)