PGS Publication: PGP000099

Publication Information (EuropePMC)
Title High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus.
PubMed ID 31826855(Europe PMC)
doi 10.1136/annrheumdis-2019-216227
Publication Date Dec. 11, 2019
Journal Ann Rheum Dis
Author(s) Reid S, Alexsson A, Frodlund M, Morris D, Sandling JK, Bolin K, Svenungsson E, Jönsen A, Bengtsson C, Gunnarsson I, Illescas Rodriguez V, Bengtsson A, Arve S, Rantapää-Dahlqvist S, Eloranta ML, Syvänen AC, Sjöwall C, Vyse TJ, Rönnblom L, Leonard D.
Released in PGS: Sept. 18, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
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

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
PPM000880 PGS000328 (GRS_SLE) PSS000436 PGP000099
Reid S et al. (2019)
Reported Trait: Systemic lupus erythematosus AUROC: 0.78 Odds Ratio (OR; highest vs. lowest quartile): 12.32[9.53, 15.71]
PPM000884 PGS000328 (GRS_SLE) PSS000436 PGP000099
Reid S et al. (2019)
Reported Trait: Systemic lupus erythematosus (age-at-onset) Hazard Ratio (HR; highest vs. lowest quartile): 1.47[1.22, 1.75]
PPM000885 PGS000328 (GRS_SLE) PSS000437 PGP000099
Reid S et al. (2019)
Reported Trait: Nephritis in systemic lupus erythematosus patients Hazard Ratio (HR; highest vs. lowest quartile): 2.53[1.72, 3.71]
PPM000881 PGS000328 (GRS_SLE) PSS000437 PGP000099
Reid S et al. (2019)
Reported Trait: Systemic lupus erythematosus (onset before age 20) AUROC: 0.83
PPM000882 PGS000328 (GRS_SLE) PSS000438 PGP000099
Reid S et al. (2019)
Reported Trait: Systemic lupus erythematosus AUROC: 0.71 Odds Ratio (OR; highest vs. lowest quartile): 7.48[6.73, 8.32]
PPM000883 PGS000328 (GRS_SLE) PSS000436 PGP000099
Reid S et al. (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]

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
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)