Polygenic Score (PGS) ID: PGS000196

Predicted Trait
Reported Trait Systemic lupus eythematosus
Mapped Trait(s) systemic lupus erythematosus (EFO_0002690)
Released in PGS: June 3, 2020

Score Details

Score Construction
PGS Name G-PROB_SLE
Variants
Original Genome Build GRCh38
Number of Variants 250
Development Method
Name Pruning and Thresholding (P+T)
Parameters SNPs with genome-wide significance (p<5e-8) from Immunobase, and LD pruning (r^2>0.8), and HLA variants incorporated in a probabilistic model that take into account predefined (sex specific) disease prevalence, and assuming a patient has one of the 5 possible arthritic diseases. See papers for detailed calculation of Gprob, and OR/weight shrinkage.
PGS Source
PGS Catalog Publication (PGP) ID PGP000081
Citation (link to publication) Knevel R et al. Sci Transl Med (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003156
EuropePMC: 26502338
14,267 individuals European
GWAS Catalog: GCST002463
EuropePMC: 24871463
3,163 individuals European
GWAS Catalog: GCST004867
EuropePMC: 19838195
9,169 individuals European

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)
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
PPM000567 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)
PPM000573 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)
PPM000579 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)

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