Polygenic Score (PGS) ID: PGS002088

Predicted Trait
Reported Trait Rheumatoid arthritis
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Additional Trait Information musculoskeletal
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_714.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 95,083
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011564 PSS009352|
European Ancestry|
18,393 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Rheumatoid arthritis — — Partial Correlation (partial-r): 0.0434 [0.029, 0.0578] sex, age, birth date, deprivation index, 16 PCs —
PPM011565 PSS009126|
European Ancestry|
3,878 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Rheumatoid arthritis — — Partial Correlation (partial-r): 0.0532 [0.0217, 0.0846] sex, age, birth date, deprivation index, 16 PCs —
PPM011566 PSS008680|
European Ancestry|
6,241 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Rheumatoid arthritis — — Partial Correlation (partial-r): 0.0284 [0.0036, 0.0532] sex, age, birth date, deprivation index, 16 PCs —
PPM011568 PSS008234|
South Asian Ancestry|
5,728 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Rheumatoid arthritis — — Partial Correlation (partial-r): 0.0135 [-0.0125, 0.0394] sex, age, birth date, deprivation index, 16 PCs —
PPM011569 PSS008014|
East Asian Ancestry|
1,754 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Rheumatoid arthritis — — Partial Correlation (partial-r): 0.0226 [-0.0245, 0.0696] sex, age, birth date, deprivation index, 16 PCs —
PPM011570 PSS007799|
African Ancestry|
2,277 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Rheumatoid arthritis — — Partial Correlation (partial-r): -0.0007 [-0.0419, 0.0406] sex, age, birth date, deprivation index, 16 PCs —
PPM011571 PSS008903|
African Ancestry|
3,634 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Rheumatoid arthritis — — Partial Correlation (partial-r): -0.0214 [-0.054, 0.0112] sex, age, birth date, deprivation index, 16 PCs —
PPM011567 PSS008454|
Greater Middle Eastern Ancestry|
1,128 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Rheumatoid arthritis — — Partial Correlation (partial-r): 0.0403 [-0.0186, 0.099] sex, age, birth date, deprivation index, 16 PCs —

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
PSS009126 — — 3,878 individuals — European Poland (NE Europe) UKB —
PSS008903 — — 3,634 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009352 — — 18,393 individuals — European UK (+ Ireland) UKB —
PSS008680 — — 6,241 individuals — European Italy (South Europe) UKB —
PSS008234 — — 5,728 individuals — South Asian India (South Asia) UKB —
PSS008454 — — 1,128 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008014 — — 1,754 individuals — East Asian China (East Asia) UKB —
PSS007799 — — 2,277 individuals — African American or Afro-Caribbean Carribean UKB —