Polygenic Score (PGS) ID: PGS001248

Predicted Trait
Reported Trait Gout
Mapped Trait(s) gout (EFO_0004274)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC328
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
Terms and Licenses
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Score Details

Score Construction
PGS Name GBE_HC328
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 880
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 5,674 cases
  • , 264,030 controls
]
European white British ancestry UKB

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
PPM008749 PSS004452|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.8285 [0.79138, 0.86562] : 0.15624
Incremental AUROC (full-covars): 0.01741
PGS R2 (no covariates): 0.02051
PGS AUROC (no covariates): 0.62118 [0.56505, 0.67731]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008750 PSS004453|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.84973 [0.79458, 0.90489] : 0.22864
Incremental AUROC (full-covars): 0.02603
PGS R2 (no covariates): 0.04315
PGS AUROC (no covariates): 0.65938 [0.56975, 0.74901]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008751 PSS004454|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.83619 [0.82126, 0.85113] : 0.17414
Incremental AUROC (full-covars): 0.02904
PGS R2 (no covariates): 0.03561
PGS AUROC (no covariates): 0.66092 [0.63744, 0.6844]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008752 PSS004455|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.77913 [0.74649, 0.81177] : 0.11671
Incremental AUROC (full-covars): 0.03258
PGS R2 (no covariates): 0.0283
PGS AUROC (no covariates): 0.63533 [0.59256, 0.6781]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008753 PSS004456|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.81572 [0.80628, 0.82516] Incremental AUROC (full-covars): 0.04061
PGS R2 (no covariates): 0.04014
: 0.15436
PGS AUROC (no covariates): 0.66908 [0.65556, 0.6826]
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
PSS004452
[
  • 93 cases
  • , 6,404 controls
]
African unspecified UKB
PSS004453
[
  • 38 cases
  • , 1,666 controls
]
East Asian UKB
PSS004454
[
  • 486 cases
  • , 24,419 controls
]
European non-white British ancestry UKB
PSS004455
[
  • 175 cases
  • , 7,656 controls
]
South Asian UKB
PSS004456
[
  • 1,484 cases
  • , 65,941 controls
]
European white British ancestry UKB Testing cohort (heldout set)