Polygenic Score (PGS) ID: PGS004064

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 megaprs.auto.GCST90013534.RA
Development Method
Name megaprs.auto
Parameters Model:Model143,Type:bolt,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:0.01,Bolt_f2:0.45,BayesR_p1:NA,BayesR_p2:NA,BayesR_p3:NA,BayesR_p4:NA
Variants
Original Genome Build GRCh38
Number of Variants 402,214
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)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90013534
Europe PMC: 33310728
 58,284 individuals European NR
GWAS Catalog: GCST90013534
Europe PMC: 33310728
 253,008 individuals East Asian NR
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
— 820 individuals European 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
PPM020035 PSS011222|
European Ancestry|
199,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Seropositive RA OR: 1.52285 [1.46263457, 1.58555171]
β: 0.42059 [0.38023931, 0.46093243]		 AUROC: 0.61325 [0.60161044, 0.62487979] R²: 0.02644 [0.02106118, 0.03159975] 0 beta = log(or)/sd_pgs
PPM020036 PSS011233|
European Ancestry|
388,890 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Seropositive RA OR: 1.6765 [1.64253856, 1.71116433]
β: 0.51671 [0.49624295, 0.53717403]		 AUROC: 0.64169 [0.63597003, 0.64740127] R²: 0.04068 [0.03737711, 0.04388012] 0 beta = log(or)/sd_pgs
PPM020037 PSS011246|
South Asian Ancestry|
44,057 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Seropositive RA OR: 2.16519 [1.63058972, 2.87505923]
β: 0.77251 [0.48894174, 1.05607327]		 AUROC: 0.68659 [0.62306752, 0.75011928] R²: 0.04033 [0.01968338, 0.06955001] 0 beta = log(or)/sd_pgs
PPM020038 PSS011262|
European Ancestry|
66,865 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Seropositive RA OR: 1.52777 [1.44093306, 1.6198353]
β: 0.42381 [0.36529086, 0.48232448]		 AUROC: 0.615 [0.59804531, 0.63195557] R²: 0.02702 [0.01945086, 0.03541182] 0 beta = log(or)/sd_pgs
PPM020039 PSS011275|
European Ancestry|
90,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Seropositive RA OR: 2.12896 [1.86473669, 2.4306247]
β: 0.75563 [0.62311986, 0.8881483]		 AUROC: 0.71237 [0.67693105, 0.74780668] R²: 0.09048 [0.06089994, 0.12628899] 0 beta = log(or)/sd_pgs

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
PSS011275 — —
[
  • 205 cases
  • , 90,069 controls
]
 — European — UKB —
PSS011246 — —
[
  • 60 cases
  • , 43,997 controls
]
 — South Asian — G&H —
PSS011222 — —
[
  • 2,384 cases
  • , 196,890 controls
]
 — European — EB —
PSS011262 — —
[
  • 1,139 cases
  • , 65,726 controls
]
 — European — HUNT —
PSS011233 RHEUMA_SEROPOS_OTH, ICD10: M05[8-9], ICD9: 7140A —
[
  • 9,332 cases
  • , 379,558 controls
]
 — European — FinnGen —