PGS Publication: PGP000509

Publication Information (EuropePMC)
Title Phenotype Risk Score but Not Genetic Risk Score Aids in Identifying Individuals With Systemic Lupus Erythematosus in the Electronic Health Record.
PubMed ID 37096581(Europe PMC)
doi 10.1002/art.42544
Publication Date July 12, 2023
Journal Arthritis Rheumatol
Author(s) Barnado A, Wheless L, Camai A, Green S, Han B, Katta A, Denny JC, Sawalha AH.
Released in PGS Catalog: Oct. 17, 2023

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003960
(GRS57_SLE)
 PGP000509 |
Barnado A et al. Arthritis Rheumatol (2023)
 Systemic lupus erythematosus systemic lupus erythematosus 57
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003960/ScoringFiles/PGS003960.txt.gz

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) 		Evaluated Score 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 PGS003960
(GRS57_SLE)
 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 PGS003960
(GRS57_SLE)
 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 PGS003960
(GRS57_SLE)
 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 PGS003960
(GRS57_SLE)
 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 PGS003960
(GRS57_SLE)
 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 PGS003960
(GRS57_SLE)
 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 —