Polygenic Score (PGS) ID: PGS002090

Predicted Trait
Reported Trait Other arthropathies
Mapped Trait(s) Arthropathy (HP_0003040)
Additional Trait Information musculoskeletal
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_716
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 859,336
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
PPM011577 PSS009354|
European Ancestry|
19,847 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0698 [0.0559, 0.0836] sex, age, birth date, deprivation index, 16 PCs —
PPM011578 PSS009128|
European Ancestry|
4,104 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0524 [0.0217, 0.0829] sex, age, birth date, deprivation index, 16 PCs —
PPM011579 PSS008682|
European Ancestry|
6,617 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0702 [0.0462, 0.0942] sex, age, birth date, deprivation index, 16 PCs —
PPM011580 PSS008456|
Greater Middle Eastern Ancestry|
1,195 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0373 [-0.0199, 0.0943] sex, age, birth date, deprivation index, 16 PCs —
PPM011582 PSS008015|
East Asian Ancestry|
1,805 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): -0.0166 [-0.0629, 0.0298] sex, age, birth date, deprivation index, 16 PCs —
PPM011583 PSS007800|
African Ancestry|
2,465 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0175 [-0.0221, 0.0571] sex, age, birth date, deprivation index, 16 PCs —
PPM011584 PSS008904|
African Ancestry|
3,893 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0202 [-0.0113, 0.0517] sex, age, birth date, deprivation index, 16 PCs —
PPM011581 PSS008236|
South Asian Ancestry|
6,278 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other arthropathies — — Partial Correlation (partial-r): 0.0588 [0.0341, 0.0834] 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
PSS009128 — — 4,104 individuals — European Poland (NE Europe) UKB —
PSS008456 — — 1,195 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008682 — — 6,617 individuals — European Italy (South Europe) UKB —
PSS009354 — — 19,847 individuals — European UK (+ Ireland) UKB —
PSS008904 — — 3,893 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008236 — — 6,278 individuals — South Asian India (South Asia) UKB —
PSS008015 — — 1,805 individuals — East Asian China (East Asia) UKB —
PSS007800 — — 2,465 individuals — African American or Afro-Caribbean Carribean UKB —