Polygenic Score (PGS) ID: PGS003960

Predicted Trait
Reported Trait Systemic lupus erythematosus
Mapped Trait(s) systemic lupus erythematosus (MONDO_0007915)
Released in PGS Catalog: Oct. 17, 2023
Download Score FTP directory
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 GRS57_SLE
Development Method
Name Genome-wide significant SNPs
Parameters NR
Variants
Original Genome Build NR
Number of Variants 57
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000509
Citation (link to publication) Barnado A et al. Arthritis Rheumatol (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 94.3%
East Asian: 5.7%
88,579 individuals (100%)
PGS Evaluation
African: 33.3%
European: 33.3%
Multi-ancestry (including European): 33.3%
  • European
  • African
  • Additional Asian Ancestries
  • Not Reported
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 22110124
[
  • 4,248 cases
  • , 3,818 controls
]
 European NR
Europe PMC: 21952918
[
  • 4,248 cases
  • , 3,818 controls
]
 European NR
GWAS Catalog: GCST003156
Europe PMC: 26502338
 14,267 individuals European NR
GWAS Catalog: GCST003622
Europe PMC: 27399966
 5,057 individuals East Asian NR
GWAS Catalog: GCST003622
Europe PMC: 27399966
 10,995 individuals European NR
GWAS Catalog: GCST007400
Europe PMC: 28714469
 18,264 individuals European NR
Europe PMC: 32077931
[
  • 5,734 cases
  • , 11,608 controls
]
 European NR
Europe PMC: 31826855
[
  • 1,001 cases
  • , 5,521 controls
]
 European NR

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
PPM019115 PSS011186|
Multi-ancestry (including European)|
3,048 individuals
 PGP000509 |
Barnado A et al. Arthritis Rheumatol (2023)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.65 [0.63, 0.67] — — —
PPM019116 PSS011188|
European Ancestry|
1,994 individuals
 PGP000509 |
Barnado A et al. Arthritis Rheumatol (2023)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.63 [0.6, 0.66] — — —
PPM019117 PSS011187|
African Ancestry|
902 individuals
 PGP000509 |
Barnado A et al. Arthritis Rheumatol (2023)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.5 [0.44, 0.56] — — —
PPM019118 PSS011186|
Multi-ancestry (including European)|
3,048 individuals
 PGP000509 |
Barnado A et al. Arthritis Rheumatol (2023)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.89 [0.87, 0.9] — phenotype risk score —
PPM019119 PSS011188|
European Ancestry|
1,994 individuals
 PGP000509 |
Barnado A et al. Arthritis Rheumatol (2023)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.87 [0.85, 0.89] — phenotype risk score —
PPM019120 PSS011187|
African Ancestry|
902 individuals
 PGP000509 |
Barnado A et al. Arthritis Rheumatol (2023)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.89 [0.86, 0.93] — phenotype risk score —

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
PSS011186 — —
[
  • 615 cases
  • , 1,379 controls
]
 — European — BioVU —
PSS011186 — —
[
  • 134 cases
  • , 768 controls
]
 — African unspecified — BioVU —
PSS011186 — —
[
  • 15 cases
  • , 45 controls
]
 — Asian unspecified — BioVU —
PSS011186 — —
[
  • 23 cases
  • , 67 controls
]
 — Not reported — BioVU —
PSS011187 — —
[
  • 134 cases
  • , 768 controls
]
 — African unspecified — BioVU —
PSS011188 — —
[
  • 615 cases
  • , 1,379 controls
]
 — European — BioVU —