Polygenic Score (PGS) ID: PGS000754

Predicted Trait
Reported Trait Systemic lupus erythematosus
Mapped Trait(s) systemic lupus erythematosus (MONDO_0007915)
Released in PGS Catalog: April 7, 2021
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Score Details

Score Construction
PGS Name PRS_SLE
Development Method
Name lassosum
Parameters s = 0.2; lambda = 0.001
Variants
Original Genome Build hg19
Number of Variants 293,684
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000160
Citation (link to publication) Wang YF et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
10,064 individuals (100%)
PGS Evaluation
European: 60%
Additional Asian Ancestries: 20%
East Asian: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90011866
[
  • 2,618 cases
  • , 7,446 controls
]
 East Asian
(Han Chinese)		 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
PPM001919 PSS000963|
East Asian Ancestry|
2,589 individuals
 PGP000160 |
Wang YF et al. Nat Commun (2021)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.76 [0.74, 0.78] — — —
PPM001920 PSS000960|
European Ancestry|
1,340 individuals
 PGP000160 |
Wang YF et al. Nat Commun (2021)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.65 — — —
PPM001921 PSS000961|
European Ancestry|
7,733 individuals
 PGP000160 |
Wang YF et al. Nat Commun (2021)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.65 — — —
PPM001922 PSS000962|
European Ancestry|
1,112 individuals
 PGP000160 |
Wang YF et al. Nat Commun (2021)
 Reported Trait: Systemic lupus erythematosus — AUROC: 0.62 — — —
PPM002076 PSS001027|
Additional Asian Ancestries|
3,996 individuals
 PGP000188 |
Tangtanatakul P et al. Arthritis Res Ther (2020)
|Ext.		 Reported Trait: Systemic lupus erythematosus — AUROC: 0.76 — — —

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
PSS000960 Cases were individuals with systemic lupus erythematosus. —
[
  • 910 cases
  • , 430 controls
]
 — European — NR —
PSS000961 Cases were individuals with systemic lupus erythematosus. —
[
  • 2,354 cases
  • , 5,379 controls
]
 — European — NR —
PSS000962 Cases were individuals with systemic lupus erythematosus. —
[
  • 406 cases
  • , 706 controls
]
 — European — NR —
PSS000963 Cases were individuals with systemic lupus erythematosus. —
[
  • 1,604 cases
  • , 985 controls
]
 — East Asian
(Han Chinese)		 — NR —
PSS001027 Cases were individuals with systemic lupus erythematosus (SLE). All cases were carefully recruited regarding the criteria from the American College of Rheumatology (ACR). Controls included healthy individuals and individuals who had unrelated diseases including: breast cancer, periodontitis, tuberculosis, drug-induced liver injury, epileptic encephalopathy, dengue hemorrhagic fever, thalassemia, and cardiomyopathy. —
[
  • 826 cases
  • , 3,170 controls
]
,
40.31 % Male samples
 — South East Asian
(Thai)		 — NR Cases were recruited from King Chulalongkorn Memorial Hospital and the Rheumatology clinic at Ramathbodi hospital. Control data was provided by the Department of Medical Science, Min- istry of Public Health, Thailand.