Polygenic Score (PGS) ID: PGS002082

Predicted Trait
Reported Trait Lupus (localized and systemic)
Mapped Trait(s) lupus erythematosus (MONDO_0004670)
Additional Trait Information dermatologic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_695.4
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 361,553
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
PPM011517 PSS009346|
European Ancestry|
19,585 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lupus (localized and systemic) — — Partial Correlation (partial-r): 0.0212 [0.0072, 0.0352] sex, age, birth date, deprivation index, 16 PCs —
PPM011518 PSS009120|
European Ancestry|
4,047 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lupus (localized and systemic) — — Partial Correlation (partial-r): 0.0268 [-0.0041, 0.0577] sex, age, birth date, deprivation index, 16 PCs —
PPM011519 PSS008674|
European Ancestry|
6,535 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lupus (localized and systemic) — — Partial Correlation (partial-r): -0.0096 [-0.0338, 0.0147] sex, age, birth date, deprivation index, 16 PCs —
PPM011520 PSS008448|
Greater Middle Eastern Ancestry|
1,184 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lupus (localized and systemic) — — Partial Correlation (partial-r): -0.0045 [-0.0619, 0.053] sex, age, birth date, deprivation index, 16 PCs —
PPM011521 PSS008228|
South Asian Ancestry|
6,185 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lupus (localized and systemic) — — Partial Correlation (partial-r): 0.005 [-0.0199, 0.03] sex, age, birth date, deprivation index, 16 PCs —
PPM011522 PSS008009|
East Asian Ancestry|
1,785 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lupus (localized and systemic) — — Partial Correlation (partial-r): 0.0076 [-0.0391, 0.0543] sex, age, birth date, deprivation index, 16 PCs —
PPM011523 PSS007793|
African Ancestry|
2,428 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lupus (localized and systemic) — — Partial Correlation (partial-r): -0.0113 [-0.0512, 0.0287] sex, age, birth date, deprivation index, 16 PCs —
PPM011524 PSS008897|
African Ancestry|
3,872 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lupus (localized and systemic) — — Partial Correlation (partial-r): -0.0062 [-0.0378, 0.0254] 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
PSS008228 — — 6,185 individuals — South Asian India (South Asia) UKB —
PSS008009 — — 1,785 individuals — East Asian China (East Asia) UKB —
PSS008674 — — 6,535 individuals — European Italy (South Europe) UKB —
PSS007793 — — 2,428 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008448 — — 1,184 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009120 — — 4,047 individuals — European Poland (NE Europe) UKB —
PSS008897 — — 3,872 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009346 — — 19,585 individuals — European UK (+ Ireland) UKB —