Polygenic Score (PGS) ID: PGS000772

Predicted Trait
Reported Trait Systemic lupus erythematosus
Mapped Trait(s) systemic lupus erythematosus (MONDO_0007915)
Released in PGS Catalog: May 28, 2021
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Score Details

Score Construction
PGS Name GRS95_SLEgen
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, R^2 < 0.1
Variants
Original Genome Build GRCh37
Number of Variants 95
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000178
Citation (link to publication) Chen L et al. Hum Mol Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 53.3%
East Asian: 32.4%
Multi-ancestry (including European): 9.1%
  • European
  • Not Reported
African: 2%
Multi-ancestry (excluding European): 2%
  • Hispanic or Latin American
  • Additional Diverse Ancestries
Hispanic or Latin American: 1.2%
184,331 individuals (100%)
Score Development/Training
European: 100%
3,076 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 24070858
[
  • 1,047 cases
  • , 1,205 controls
]
,
32.68 % Male samples
 East Asian
(Han-Chinese)		 NR
GWAS Catalog: GCST003155
Europe PMC: 26502338
 14,267 individuals European NR
GWAS Catalog: GCST000507
Europe PMC: 19838193
 2,252 individuals East Asian NR
Europe PMC: 25890262
[
  • 1,047 cases
  • , 1,205 controls
]
,
32.68 % Male samples
 East Asian
(Han-Chinese)		 NR
Europe PMC: 24163247
[
  • 1,476 cases
  • , 14,661 controls
]
 European CCHMC, GENYO
GWAS Catalog: GCST002463
Europe PMC: 24871463
 3,163 individuals European Illumina_iControlDB
GWAS Catalog: GCST003622
Europe PMC: 27399966
 10,995 individuals European NR
GWAS Catalog: GCST001795
Europe PMC: 23273568
 5,050 individuals East Asian NR
Europe PMC: 25620976
[
  • 4,220 cases
  • , 3,803 controls
]
,
21.14 % Male samples
 European NR
Europe PMC: 22464253
[
  • 3,936 cases
  • , 3,491 controls
]
 European NR
GWAS Catalog: GCST002845
Europe PMC: 25862617
 5,050 individuals East Asian NR
Europe PMC: 28108556
[
  • 4,478 cases
  • , 15,246 controls
]
 East Asian
(Chinese, Han-Chinese)		 NR
GWAS Catalog: GCST001384
Europe PMC: 22291604
 4,275 individuals East Asian NR
Europe PMC: 21425124
[
  • 4,248 cases
  • , 3,818 controls
]
 European NR
Europe PMC: 26808113
[
  • 2,487 cases
  • , 7,616 controls
]
,
36.91 % Male samples
 East Asian
(Chinese, Han-Chinese, Korean)		 NR
Europe PMC: 22046141
[
  • 3,273 cases
  • , 12,188 controls
]
 European, NR NR
GWAS Catalog: GCST000142
Europe PMC: 18204446
 3,037 individuals European Illumina_iControlDB, UCSF, USC
GWAS Catalog: GCST003252
Europe PMC: 26606652
 3,710 individuals Hispanic or Latin American, Native American NR
Europe PMC: 21194677
[
  • 431 cases
  • , 2,155 controls
]
 European NR
GWAS Catalog: GCST003103
Europe PMC: 26316170
 1,148 individuals European NR
Europe PMC: 21134959
[
  • 1,047 cases
  • , 1,205 controls
]
,
6.02 % Male samples
 East Asian
(Han-Chinese)		 NR
Europe PMC: 22523428
[
  • 3,936 cases
  • , 3,491 controls
]
 European 8 cohorts
  • CCHMC
  • ,GENYO
  • ,UAB
  • ,UCLA
  • ,UCSF
  • ,UMN
  • ,USC
  • ,WASHU
Europe PMC: 22523428
[
  • 1,679 cases
  • , 1,934 controls
]
 African unspecified 6 cohorts
  • CCHMC
  • ,UAB
  • ,UCLA
  • ,USC
  • ,WASHU
  • ,WFSM
Europe PMC: 22523428
[
  • 1,492 cases
  • , 807 controls
]
 Hispanic or Latin American 6 cohorts
  • CCHMC
  • ,GENYO
  • ,UAB
  • ,UCLA
  • ,USC
  • ,WASHU
Europe PMC: 22523428
[
  • 640 cases
  • , 740 controls
]
 East Asian NR
Europe PMC: 21914625
[
  • 509 cases
  • , 825 controls
]
 European, NR NR
Europe PMC: 17997607
[
  • 314 cases
  • , 1,667 controls
]
 European NR
GWAS Catalog: GCST003622
Europe PMC: 27399966
 5,057 individuals East Asian NR
GWAS Catalog: GCST004867
Europe PMC: 19838195
 9,169 individuals European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 533 cases
  • , 2,543 controls
]
 European NR Cases were individuals with systemic lupus erythematosus. 524 case individuals provided information on renal status. Of the 524 individuals, 146 had renal disease. — — — Cases and controls obtained by SLEGEN.

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
PPM001997 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

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
PSS000993 All individuals had systemic lupus erythematosus. Cases are individuals that also have renal disease —
[
  • 1,152 cases
  • , 1,949 controls
]
 — European — NR —