Polygenic Score (PGS) ID: PGS004873

Predicted Trait
Reported Trait Rheumatoid arthritis
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Released in PGS Catalog: June 27, 2024
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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 INTERVENE_MegaPRS_RA
Development Method
Name megaprs.auto
Parameters BayesR, p1=0.795, p2=0.2, p3=0.005, p4=0
Variants
Original Genome Build GRCh37
Number of Variants 551,074
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000618
Citation (link to publication) Jermy B et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 81.3%
European: 18.7%
311,292 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
8 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
— 404 individuals European 1000G — — — non-Finnish Europeans —

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
PPM021165 PSS011635|
European Ancestry|
447,332 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident RA HR: 1.87 [1.76, 1.99] — — PCs 1-10 —
PPM021166 PSS011634|
European Ancestry|
37,986 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident RA HR: 2.16 [1.96, 2.37] C-index: 0.71 [0.68, 0.74] — PCs 1-10 —
PPM021167 PSS011633|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident RA HR: 1.59 [1.49, 1.68] C-index: 0.64 [0.62, 0.66] — PCs 1-10 —
PPM021168 PSS011632|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident RA HR: 2.27 [1.81, 2.84] C-index: 0.73 [0.66, 0.8] — PCs 1-10 —
PPM021169 PSS011630|
European Ancestry|
44,188 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident RA HR: 2.13 [1.65, 2.75] — — PCs 1-10 —
PPM021170 PSS011631|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident RA HR: 1.83 [1.14, 2.93] C-index: 0.85 [0.77, 0.92] — PCs 1-10 —
PPM021171 PSS011629|
European Ancestry|
412,090 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident RA HR: 1.65 [1.62, 1.69] C-index: 0.65 [0.65, 0.66] — PCs 1-10 —
PPM021172 PSS011628|
European Ancestry|
199,868 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident RA HR: 1.43 [1.38, 1.49] C-index: 0.61 [0.6, 0.62] — PCs 1-10 —

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
PSS011628 — —
[
  • 2,348 cases
  • , 197,520 controls
]
 — European — EB —
PSS011629 — —
[
  • 9,610 cases
  • , 402,480 controls
]
 — European — FinnGen —
PSS011630 — —
[
  • 58 cases
  • , 44,130 controls
]
 — European — G&H —
PSS011631 — —
[
  • 18 cases
  • , 7,000 controls
]
 — European — GS:SFHS —
PSS011632 — —
[
  • 71 cases
  • , 29,356 controls
]
 — European — GEL —
PSS011633 — —
[
  • 1,072 cases
  • , 68,643 controls
]
 — European — HUNT —
PSS011634 — —
[
  • 384 cases
  • , 37,602 controls
]
 — European — MGBB —
PSS011635 — —
[
  • 994 cases
  • , 446,338 controls
]
 — European — UKB —