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 Number of Variants PGS Scoring File (FTP Link)
PGS000196 G-PROB_SLE PGP000081
Knevel R et al. Sci Transl Med (2020)
Systemic lupus eythematosus 250 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000196/ScoringFiles/PGS000196.txt.gz

PGS 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. (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. (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. (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)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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 PHCB
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
Other Primarily European, African and Asian ancestry eMERGE
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 PHCB