Polygenic Score (PGS) ID: PGS001789

Predicted Trait
Reported Trait Gout
Mapped Trait(s) gout (EFO_0004274)
Released in PGS Catalog: Sept. 8, 2022
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Score Details

Score Construction
PGS Name 1kgeur_gbmi_leaveUKBBout_Gout_pst_eff_a1_b0.5_phiauto
Development Method
Name PRS-CS-auto
Parameters effective sample size and other defualt parameters
Variants
Original Genome Build GRCh37
Number of Variants 910,151
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000262
Citation (link to publication) Wang Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 60.2%
East Asian: 33.3%
African: 2.7%
Additional Asian Ancestries: 2.1%
Additional Diverse Ancestries: 1.7%
1,049,659 individuals (100%)
PGS Evaluation
African: 33.3%
Additional Asian Ancestries: 33.3%
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 1,255 cases
  • , 27,326 controls
]
African unspecified G&H
[
  • 557 cases
  • , 17,629 controls
]
Native American BioMe, BioVU, MGI, UCLA
[
  • 10,425 cases
  • , 338,934 controls
]
East Asian BioMe, UCLA
[
  • 19,769 cases
  • , 611,816 controls
]
European BBJ, CKB, UCLA
[
  • 421 cases
  • , 21,527 controls
]
Asian unspecified 11 cohorts
  • BioMe
  • ,BioVU
  • ,CCPM
  • ,EB
  • ,FinnGen
  • ,GS:SFHS
  • ,HUNT
  • ,LifeLines
  • ,MGBB
  • ,MGI
  • ,UCLA

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
PPM009309 PSS007699|
African Ancestry|
6,206 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.805 Nagelkerke's R2 (covariates regressed out): 0.01073 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009293 PSS007712|
European Ancestry|
359,345 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.807 Nagelkerke's R2 (covariates regressed out): 0.03121 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009304 PSS007703|
Additional Asian Ancestries|
8,184 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.78 Nagelkerke's R2 (covariates regressed out): 0.00748 sex,age,age2,age*sex,age^2*sex, 20PCs

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
PSS007703
[
  • 97 cases
  • , 8,086 controls
]
Asian unspecified Central and South Asian UKB
PSS007712
[
  • 3,783 cases
  • , 355,561 controls
]
European UKB
PSS007699
[
  • 54 cases
  • , 6,151 controls
]
African unspecified Africa or admixed-ancestry diaspora UKB