PGS Publication: PGP000178

Publication Information (EuropePMC)
Title Genome-wide assessment of genetic risk for systemic lupus erythematosus and disease severity.
PubMed ID 32077931(Europe PMC)
doi 10.1093/hmg/ddaa030
Publication Date June 1, 2020
Journal Hum Mol Genet
Author(s) Chen L, Wang YF, Liu L, Bielowka A, Ahmed R, Zhang H, Tombleson P, Roberts AL, Odhams CA, Cunninghame Graham DS, Zhang X, Yang W, Vyse TJ, Morris DL.
Released in PGS Catalog: May 28, 2021

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)
PGS000771
(GRS95_SLEmain)
 PGP000178 |
Chen L et al. Hum Mol Genet (2020)
 Systemic lupus erythematosus systemic lupus erythematosus 95
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000771/ScoringFiles/PGS000771.txt.gz
PGS000772
(GRS95_SLEgen)
 PGP000178 |
Chen L et al. Hum Mol Genet (2020)
 Systemic lupus erythematosus systemic lupus erythematosus 95
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000772/ScoringFiles/PGS000772.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
PPM001996 PGS000771
(GRS95_SLEmain)
 PSS000994|
European Ancestry|
524 individuals
 PGP000178 |
Chen L et al. Hum Mol Genet (2020)
 Reported Trait: Renal disease age of onset — AUROC: 0.576 [0.518, 0.634] — — Renal disease is used as a proxy for systemic lupus erythematosus severity
PPM001997 PGS000772
(GRS95_SLEgen)
 PSS000993|
European Ancestry|
3,101 individuals
 PGP000178 |
Chen L et al. Hum Mol Genet (2020)
 Reported Trait: Renal disease — — Odds Ratio (OR, top 20% vs bottom 20%): 1.578 [1.25, 1.991] — Renal disease is used as a proxy for systemic lupus erythematosus severity
PPM001998 PGS000771
(GRS95_SLEmain)
 PSS000994|
European Ancestry|
524 individuals
 PGP000178 |
Chen L et al. Hum Mol Genet (2020)
 Reported Trait: Renal disease age of onset — — Odds Ratio (OR, top 20% vs bottom 20%): 3.155 [1.623, 6.133] — Renal disease is used as a proxy for systemic lupus erythematosus severity

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
PSS000994 All individuals had systemic lupus erythematosus. Cases are individuals that also have renal disease —
[
  • 146 cases
  • , 378 controls
]
 — European — NR Cases and controls obtained by SLEGEN.
PSS000993 All individuals had systemic lupus erythematosus. Cases are individuals that also have renal disease —
[
  • 1,152 cases
  • , 1,949 controls
]
 — European — NR —