Polygenic Score (PGS) ID: PGS000196

Predicted Trait
Reported Trait Systemic lupus erythematosus
Mapped Trait(s) systemic lupus erythematosus (MONDO_0007915)
Released in PGS Catalog: June 3, 2020
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Score Details

Score Construction
PGS Name G-PROB_SLE
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.
Variants
Original Genome Build GRCh38
Number of Variants 55
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000081
Citation (link to publication) Knevel R et al. Sci Transl Med (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
26,599 individuals (100%)
PGS Evaluation
European: 66.7%
Multi-ancestry (including European): 33.3%
  • European
  • African
  • Additional Asian Ancestries
  • Not Reported
3 Sample Sets

Development Samples

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

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
PPM000579 PSS000319|
European Ancestry|
243 individuals
 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 PSS000318|
European Ancestry|
245 individuals
 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 PSS000324|
Multi-ancestry (including European)|
1,211 individuals
 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)

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
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 —
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 —