Polygenic Score (PGS) ID: PGS004917

Predicted Trait
Reported Trait Systemic lupus erythematosus
Mapped Trait(s) systemic lupus erythematosus (MONDO_0007915)
Released in PGS Catalog: June 12, 2024
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Score Details

Score Construction
PGS Name wGRS
Development Method
Name Clumping of genome-wide significant variants
Parameters P ≤ 5e-8, R^2 ≤ 0.3
Variants
Original Genome Build NR
Number of Variants 97
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000648
Citation (link to publication) Cui J et al. Arthritis Rheumatol (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 79.2%
East Asian: 20.8%
116,600 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • Not Reported
  • Additional Asian Ancestries
  • African
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST000142
Europe PMC: 18204446
3,037 individualsEuropeanNR
GWAS Catalog: GCST000216
Europe PMC: 19165918
2,586 individualsEuropeanNR
GWAS Catalog: GCST000507
Europe PMC: 19838193
2,252 individualsEast AsianNR
GWAS Catalog: GCST001384
Europe PMC: 22291604
4,275 individualsEast AsianNR
GWAS Catalog: GCST001795
Europe PMC: 23273568
5,050 individualsEast AsianNR
GWAS Catalog: GCST002463
Europe PMC: 24871463
3,163 individualsEuropeanNR
GWAS Catalog: GCST003155
Europe PMC: 26502338
14,267 individualsEuropeanNR
GWAS Catalog: GCST003156
Europe PMC: 26502338
14,267 individualsEuropeanNR
GWAS Catalog: GCST003599
Europe PMC: 26663301
5,420 individualsEast AsianNR
GWAS Catalog: GCST003620
Europe PMC: 27193031
16,546 individualsEuropeanNR
GWAS Catalog: GCST003622
Europe PMC: 27399966
5,057 individualsEast AsianNR
GWAS Catalog: GCST003622
Europe PMC: 27399966
10,995 individualsEuropeanNR
GWAS Catalog: GCST004867
Europe PMC: 19838195
9,169 individualsEuropeanNR
GWAS Catalog: GCST005754
Europe PMC: 29494758
2,252 individualsEast AsianNR
GWAS Catalog: GCST007400
Europe PMC: 28714469
18,264 individualsEuropeanNR
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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.

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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
PPM021383PSS011718|
Multi-ancestry (including European)|
3,945 individuals
PGP000648 |
Cui J et al. Arthritis Rheumatol (2020)
Reported Trait: Systemic lupus erythematosusOR: 2.01 [1.83, 2.22]
β: 0.7 (0.05)
AUROC: 0.696
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Evaluated Samples

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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
PSS011718Those indicating having received a new systemic lupus erythematosus diagnosis were asked to complete...  the Connective Tissue Disease Screening Question- naire (12) and to consent to the release of their medical records. Released medical records of all nurses who indicated experi- encing systemic lupus erythematosus symptoms on this questionnaire were independently reviewed by 3 board-certified rheumatologists (EWK, JAS, and KHC). Cases of systemic lupus erythematosus were identified based on the presence of at least 4 criteria from the American College of Rheumatology (ACR) 1997 updated criteria for the classification of SLE and also based on reviewers' consensus.Show more
[
  • 138 cases
  • , 1,136 controls
]
,
0.0 % Male samples
European, Not reportedEuropean (98%)NHS, NHS2
PSS011718All patients diagnosed as having systemic lupus erythematosus in the PHB and included in this study...  met at least 4 of the 11 ACR 1997 updated classification criteria for systemic lupus erythematosus . Cases were identified as those individuals previously included in the Brigham and Women's Hospital Lupus Registry or those with ≥3 Interna- tional Classification of Diseases, Ninth Revision (ICD-9)/ICD-10 codes for systemic lupus erythematosus , each noted ≥30 days apart, followed by medical record review to identify the presence of any of the ACR 1997 criteria for systemic lupus erythematosus.Show more
[
  • 535 cases
  • , 2,136 controls
]
,
9.7 % Male samples
European, Asian unspecified, African unspecified, Not reportedEuropean (68.1%), Asian (4.9%), African (14.2%), Not reported (12.8%)PHB
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