Polygenic Score (PGS) ID: PGS001293

Predicted Trait
Reported Trait Other diseases of liver (time-to-event)
Mapped Trait(s) liver disease (EFO_0001421)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1123
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_HC1123
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 92
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
—
[
  • 4,680 cases
  • , 265,024 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
PPM008963 PSS004134|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.63246 [0.57311, 0.69181] R²: 0.03109
Incremental AUROC (full-covars): -0.0062
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50545 [0.44895, 0.56196]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008964 PSS004135|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.69904 [0.62545, 0.77263] PGS R2 (no covariates): 0.01113
Incremental AUROC (full-covars): 0.02137
R²: 0.05749
PGS AUROC (no covariates): 0.60324 [0.52305, 0.68342]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008965 PSS004136|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.63842 [0.61377, 0.66307] R²: 0.02524
Incremental AUROC (full-covars): 0.02435
PGS R2 (no covariates): 0.01187
PGS AUROC (no covariates): 0.59189 [0.56464, 0.61913]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008966 PSS004137|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.60451 [0.56674, 0.64227] R²: 0.01731
Incremental AUROC (full-covars): 0.00746
PGS R2 (no covariates): 0.00179
PGS AUROC (no covariates): 0.53523 [0.49417, 0.57629]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008967 PSS004138|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.58372 [0.56726, 0.60017] R²: 0.00961
Incremental AUROC (full-covars): 0.01977
PGS R2 (no covariates): 0.00443
PGS AUROC (no covariates): 0.5536 [0.53634, 0.57086]		 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
PSS004134 — —
[
  • 93 cases
  • , 6,404 controls
]
 — African unspecified — UKB —
PSS004135 — —
[
  • 37 cases
  • , 1,667 controls
]
 — East Asian — UKB —
PSS004136 — —
[
  • 460 cases
  • , 24,445 controls
]
 — European non-white British ancestry UKB —
PSS004137 — —
[
  • 193 cases
  • , 7,638 controls
]
 — South Asian — UKB —
PSS004138 — —
[
  • 1,158 cases
  • , 66,267 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)