Trait: systemic lupus erythematosus

Experimental Factor Ontology (EFO) Information
Identifier EFO_0002690
Description An autoimmune multi-organ disease typically associated with vasculopathy and autoantibody production. Most patients have antinuclear antibodies (ANA). The presence of anti-dsDNA or anti-Smith antibodies are highly-specific. [NCIT: P378]
Trait category
Immune system disorder
Synonyms 13 synonyms
  • Disease, Libman-Sacks
  • LIBMAN SACKS DIS
  • Libman Sacks Disease
  • Libman-Sacks Disease
  • Lupus Erythematosus Disseminatus
  • Lupus Erythematosus, Systemic
  • SLE
  • SLE - lupus erythematosus, systemic
  • disseminated lupus erythematosus
  • lupus
  • lupus erythematosus, systemic
  • systemic lupus erythematosus
  • systemic lupus erythematosus (disease)
Mapped term(s) 26 mapped terms
  • COHD:257628
  • DOID:9074
  • EV:0400043
  • HP:0002725
  • ICD10:M32
  • ICD10:M32.0
  • ICD10:M32.1
  • ICD10:M32.8
  • ICD10:M32.9
  • ICD9:710.0
  • KEGG:05322
  • MESH:D008180
  • MONDO:0007915
  • MSH:D008180
  • NCIT:C3201
  • NCIt:C3201
  • OMIM:152700
  • OMIM:601744
  • OMIM:605218
  • OMIM:609939
  • OMIM:610927
  • OMIM:612251
  • OMIM:612253
  • Orphanet:536
  • SCTID:55464009
  • SNOMEDCT:55464009

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000196 G-PROB_SLE PGP000081
Knevel R et al. Sci Transl Med (2020)
Systemic lupus eythematosus systemic lupus erythematosus 250 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000196/ScoringFiles/PGS000196.txt.gz
PGS000328 GRS_SLE PGP000099
Reid S et al. Ann Rheum Dis (2019)
Systemic lupus erythematosus systemic lupus erythematosus 57 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000328/ScoringFiles/PGS000328.txt.gz
PGS000754 PRS_SLE PGP000160
Wang YF et al. Nat Commun (2021)
Systemic lupus erythrmatosus systemic lupus erythematosus 293,684 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000754/ScoringFiles/PGS000754.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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000579 PGS000196
(G-PROB_SLE)
PSS000319 PGP000081
Knevel R et al. Sci Transl Med (2020)
Reported Trait: Systemic lupus erythematosus diagnosis in patient with arthritis AUROC: 0.61 [0.27, 0.86] (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000573 PGS000196
(G-PROB_SLE)
PSS000318 PGP000081
Knevel R et al. Sci Transl Med (2020)
Reported Trait: Systemic lupus erythematosus diagnosis in patient with arthritis AUROC: 0.79 [0.72, 0.85] (Setting II: Assigning patient diagnoses based on medical records)
PPM000567 PGS000196
(G-PROB_SLE)
PSS000324 PGP000081
Knevel R et al. Sci Transl Med (2020)
Reported Trait: Systemic lupus erythematosus diagnosis in patient with arthritis AUROC: 0.74 [0.7, 0.78] (Setting I: Assigning patient diagnoses based on billing codes)
PPM000882 PGS000328
(GRS_SLE)
PSS000438 PGP000099
Reid S et al. Ann Rheum Dis (2019)
Reported Trait: Systemic lupus erythematosus AUROC: 0.71 Odds Ratio (OR; highest vs. lowest quartile): 7.48 [6.73, 8.32]
PPM000880 PGS000328
(GRS_SLE)
PSS000436 PGP000099
Reid S et al. Ann Rheum Dis (2019)
Reported Trait: Systemic lupus erythematosus AUROC: 0.78 Odds Ratio (OR; highest vs. lowest quartile): 12.32 [9.53, 15.71]
PPM000883 PGS000328
(GRS_SLE)
PSS000436 PGP000099
Reid S et al. Ann Rheum Dis (2019)
Reported Trait: Systemic Lupus damage score (SDI) OR: 1.13 [1.03, 1.24] Odds Ratio (OR; highest vs. lowest quartile): 1.47 [1.06, 2.04]
PPM000881 PGS000328
(GRS_SLE)
PSS000437 PGP000099
Reid S et al. Ann Rheum Dis (2019)
Reported Trait: Systemic lupus erythematosus (onset before age 20) AUROC: 0.83
PPM000885 PGS000328
(GRS_SLE)
PSS000437 PGP000099
Reid S et al. Ann Rheum Dis (2019)
Reported Trait: Nephritis in systemic lupus erythematosus patients Hazard Ratio (HR; highest vs. lowest quartile): 2.53 [1.72, 3.71]
PPM000884 PGS000328
(GRS_SLE)
PSS000436 PGP000099
Reid S et al. Ann Rheum Dis (2019)
Reported Trait: Systemic lupus erythematosus (age-at-onset) Hazard Ratio (HR; highest vs. lowest quartile): 1.47 [1.22, 1.75]
PPM001919 PGS000754
(PRS_SLE)
PSS000963 PGP000160
Wang YF et al. Nat Commun (2021)
Reported Trait: Systemic lupus erythematosus AUROC: 0.76 [0.74, 0.78]
PPM001920 PGS000754
(PRS_SLE)
PSS000960 PGP000160
Wang YF et al. Nat Commun (2021)
Reported Trait: Systemic lupus erythematosus AUROC: 0.65
PPM001921 PGS000754
(PRS_SLE)
PSS000961 PGP000160
Wang YF et al. Nat Commun (2021)
Reported Trait: Systemic lupus erythematosus AUROC: 0.65
PPM001922 PGS000754
(PRS_SLE)
PSS000962 PGP000160
Wang YF et al. Nat Commun (2021)
Reported Trait: Systemic lupus erythematosus AUROC: 0.62

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000436 The discovery cohort included 1001 patients from the University clinics in Uppsala, Linköping, Karolinska Institute (Stockholm), Lund, and from the four northern-most counties in Sweden. All subjects fulfilled ≥4 ACR-82 classification criteria for SLE and were of European descent.30 Clinical data were collected from the patients’ medical files, including SDI scores, the ACR-82 classification criteria, clinical antiphospholipid syndrome (APS) diagnosis, glomerular filtration rate, chronic kidney disease (CKD) stages, ESRD, renal biopsy data and CVE, defined as myocardial infarction, ischaemic cerebrovascular disease or venous thromboembolism (VTE). Control individuals were healthy blood donors from Uppsala (Uppsala Bioresource) and Lund or population based controls from Stockholm and the four northernmost counties of Sweden.
[
  • 1,001 cases
  • , 2,802 controls
]
European Karolinska, UHU The discovery cohort included 1001 patients from the University clinics in Uppsala, Linköping, Karolinska Institute (Stockholm), Lund, and from the four northern-most counties in Sweden
PSS000437 The discovery cohort included 1001 patients from the University clinics in Uppsala, Linköping, Karolinska Institute (Stockholm), Lund, and from the four northern-most counties in Sweden. All subjects fulfilled ≥4 ACR-82 classification criteria for SLE and were of European descent.30 Clinical data were collected from the patients’ medical files, including SDI scores, the ACR-82 classification criteria, clinical antiphospholipid syndrome (APS) diagnosis, glomerular filtration rate, chronic kidney disease (CKD) stages, ESRD, renal biopsy data and CVE, defined as myocardial infarction, ischaemic cerebrovascular disease or venous thromboembolism (VTE).
[
  • 1,001 cases
  • , 0 controls
]
European Karolinska, UHU The discovery cohort included 1001 patients from the University clinics in Uppsala, Linköping, Karolinska Institute (Stockholm), Lund, and from the four northern-most counties in Sweden
PSS000438
[
  • 5,524 cases
  • , 9,859 controls
]
European The replication cohort is described in Langefeld et al. (PMID:28714469)
PSS000963 Cases were individuals with systemic lupus erythematosus.
[
  • 1,604 cases
  • , 985 controls
]
East Asian
(Han Chinese)
PSS000961 Cases were individuals with systemic lupus erythematosus.
[
  • 2,354 cases
  • , 5,379 controls
]
European
PSS000962 Cases were individuals with systemic lupus erythematosus.
[
  • 406 cases
  • , 706 controls
]
European
PSS000318 Setting II: Based on ICD codes and review of medical records from Partners HealthCare Biobank; controls = other non-matching arthritis diseases Median = 8.0 years
[
  • 62 cases
  • , 183 controls
]
,
32.0 % Male samples
European PHB
PSS000319 Setting III: Based on ICD codes and final diagnosis in medical records from Partners HealthCare Biobank; controls = other non-matching arthritis diseases Median = 7.0 years
[
  • 7 cases
  • , 236 controls
]
,
32.0 % Male samples
European PHB
PSS000324 Setting I: Based on ICD codes and expert opinion (ACR2010 criteria), in eMERGE network EMR database from Stanaway 2018; controls = other non-matching arthritis diseases Median = 16.0 years
[
  • 133 cases
  • , 1,078 controls
]
,
43.0 % Male samples
European, African unspecified, Asian unspecified, NR Primarily European, African and Asian ancestry eMERGE