Polygenic Score (PGS) ID: PGS001174

Predicted Trait
Reported Trait Cholelithiasis (time-to-event)
Mapped Trait(s) cholelithiasis (EFO_0004799)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1125
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_HC1125
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 970
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
—
[
  • 15,061 cases
  • , 254,643 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
PPM008580 PSS004139|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.69202 [0.6517, 0.73234] R²: 0.05473
Incremental AUROC (full-covars): 0.01651
PGS R2 (no covariates): 0.00765
PGS AUROC (no covariates): 0.56963 [0.52438, 0.61487]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008581 PSS004140|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.69749 [0.6348, 0.76018] R²: 0.06838
Incremental AUROC (full-covars): 0.01442
PGS R2 (no covariates): 0.00347
PGS AUROC (no covariates): 0.557 [0.48585, 0.62815]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008582 PSS004141|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.66706 [0.6514, 0.68272] R²: 0.05295
Incremental AUROC (full-covars): 0.04311
PGS R2 (no covariates): 0.02808
PGS AUROC (no covariates): 0.62342 [0.60688, 0.63996]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008583 PSS004142|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.68516 [0.65563, 0.7147] R²: 0.05864
Incremental AUROC (full-covars): 0.01084
PGS R2 (no covariates): 0.00661
PGS AUROC (no covariates): 0.55746 [0.52498, 0.58993]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008584 PSS004143|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.67421 [0.66558, 0.68284] R²: 0.05848
Incremental AUROC (full-covars): 0.04052
PGS R2 (no covariates): 0.02571
PGS AUROC (no covariates): 0.61632 [0.60704, 0.62561]		 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
PSS004139 — —
[
  • 158 cases
  • , 6,339 controls
]
 — African unspecified — UKB —
PSS004140 — —
[
  • 65 cases
  • , 1,639 controls
]
 — East Asian — UKB —
PSS004141 — —
[
  • 1,175 cases
  • , 23,730 controls
]
 — European non-white British ancestry UKB —
PSS004142 — —
[
  • 312 cases
  • , 7,519 controls
]
 — South Asian — UKB —
PSS004143 — —
[
  • 3,753 cases
  • , 63,672 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)