Polygenic Score (PGS) ID: PGS004094

Predicted Trait
Reported Trait Rheumatoid arthritis
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Additional Trait Information seropositive RA
Released in PGS Catalog: Dec. 19, 2023
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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 prscs.auto.GCST90013534.RA
Development Method
Name PRS-CS-auto
Parameters phi:auto
Variants
Original Genome Build GRCh38
Number of Variants 755,048
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 81.3%
European: 18.7%
311,292 individuals (100%)
Score Development/Training
European: 100%
820 individuals (100%)
PGS Evaluation
European: 80%
South Asian: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST90013534
Europe PMC: 33310728
58,284 individualsEuropeanNR
GWAS Catalog: GCST90013534
Europe PMC: 33310728
253,008 individualsEast AsianNR
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Score Development/Training
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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
—820 individualsEuropeanUKB—————
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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.

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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
PPM020045PSS011222|
European Ancestry|
199,274 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Seropositive RAOR: 1.43309 [1.37789918, 1.49048299]
β: 0.35983 [0.32056001, 0.39910022]		AUROC: 0.60175 [0.58999494, 0.61350437]R²: 0.01993 [0.01570594, 0.02462764]0beta = log(or)/sd_pgs
PPM020046PSS011233|
European Ancestry|
388,890 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Seropositive RAOR: 1.64768 [1.61352054, 1.68256451]
β: 0.49937 [0.47841846, 0.52031912]		AUROC: 0.63372 [0.62788781, 0.63955506]R²: 0.03632 [0.03309896, 0.03953108]0beta = log(or)/sd_pgs
PPM020047PSS011246|
South Asian Ancestry|
44,057 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Seropositive RAOR: 1.45841 [1.19873228, 1.77432944]
β: 0.37734 [0.18126456, 0.57342257]		AUROC: 0.60742 [0.53398957, 0.68084175]R²: 0.01948 [0.00432876, 0.05204534]0beta = log(or)/sd_pgs
PPM020048PSS011262|
European Ancestry|
66,865 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Seropositive RAOR: 1.30074 [1.2314019, 1.37398385]
β: 0.26293 [0.20815328, 0.31771444]		AUROC: 0.58564 [0.56934416, 0.60192786]R²: 0.01181 [0.00719488, 0.01742899]0beta = log(or)/sd_pgs
PPM020049PSS011275|
European Ancestry|
90,274 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Seropositive RAOR: 1.88898 [1.67167849, 2.13453009]
β: 0.63604 [0.5138282, 0.75824653]		AUROC: 0.69466 [0.65809177, 0.73122596]R²: 0.07313 [0.04487877, 0.10829372]0beta = log(or)/sd_pgs
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Evaluated Samples

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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
PSS011222——
[
  • 2,384 cases
  • , 196,890 controls
]
—European—EB—
PSS011233RHEUMA_SEROPOS_OTH, ICD10: M05[8-9], ICD9: 7140A—
[
  • 9,332 cases
  • , 379,558 controls
]
—European—FinnGen—
PSS011246——
[
  • 60 cases
  • , 43,997 controls
]
—South Asian—G&H—
PSS011262——
[
  • 1,139 cases
  • , 65,726 controls
]
—European—HUNT—
PSS011275——
[
  • 205 cases
  • , 90,069 controls
]
—European—UKB—
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