Polygenic Score (PGS) ID: PGS003755

Predicted Trait
Reported Trait Systemic lupus erythematosus
Mapped Trait(s) systemic lupus erythematosus (MONDO_0007915)
Released in PGS Catalog: June 22, 2023
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Score Details

Score Construction
PGS Name wGRS_SLE
Development Method
Name Genome-wide significant SNPs; HLA-DRB1 specific haplotypes
Parameters NR
Variants
Original Genome Build NR
Number of Variants 122
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000475
Citation (link to publication) Kwon YC et al. Arthritis Rheumatol (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
213,712 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST011956
Europe PMC: 33272962
 208,370 individuals East Asian NR
Europe PMC: 25533202
[
  • 849 cases
  • , 4,493 controls
]
 East Asian
(Korean)		 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
PPM018525 PSS011006|
East Asian Ancestry|
1,655 individuals
 PGP000475 |
Kwon YC et al. Arthritis Rheumatol (2023)
 Reported Trait: Class III/IV lupus nephritis in anti-sm positive systemic lupus erythematosus — AUROC: 0.582 [0.496, 0.668] — — —
PPM018519 PSS011006|
East Asian Ancestry|
1,655 individuals
 PGP000475 |
Kwon YC et al. Arthritis Rheumatol (2023)
 Reported Trait: Childhood-onset systemic lupus erythematosus (onset at age <16 years) — — p: 6.80e-08 — —
PPM018520 PSS011006|
East Asian Ancestry|
1,655 individuals
 PGP000475 |
Kwon YC et al. Arthritis Rheumatol (2023)
 Reported Trait: Number of American College of Rheumatology (ACR) criteria for systemic lupus erythematosus β: 0.143 [0.078, 0.208] — — Onset age, sex, disease duration, and top 4 principal components —
PPM018523 PSS011006|
East Asian Ancestry|
1,655 individuals
 PGP000475 |
Kwon YC et al. Arthritis Rheumatol (2023)
 Reported Trait: Renal disorder β: 1.22 [1.12, 1.33] — — Onset age, sex, disease duration, and top 4 principal components —
PPM018524 PSS011006|
East Asian Ancestry|
1,655 individuals
 PGP000475 |
Kwon YC et al. Arthritis Rheumatol (2023)
 Reported Trait: Production of anti-Sm antibody β: 1.23 [1.11, 1.36] — — Onset age, sex, disease duration, and top 4 principal components —
PPM018526 PSS011006|
East Asian Ancestry|
1,655 individuals
 PGP000475 |
Kwon YC et al. Arthritis Rheumatol (2023)
 Reported Trait: Class V lupus nephritis in anti-sm positive systemic lupus erythematosus — AUROC: 0.681 [0.602, 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
PSS011006 — — 1,655 individuals,
8.4 % Male samples
 Mean = 38.1 years
Sd = 12.5 years		 East Asian
(Korean)		 — NR —