| Predicted Trait | |
| Reported Trait | Systemic lupus erythematosus |
| Mapped Trait(s) | systemic lupus erythematosus (MONDO_0007915) |
| 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 | |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST007400 Europe PMC: 28714469 |
18,264 individuals | European | NR |
GWAS Catalog: GCST003156 Europe PMC: 26502338 |
14,267 individuals | European | NR |
GWAS Catalog: GCST003155 Europe PMC: 26502338 |
14,267 individuals | European | NR |
GWAS Catalog: GCST003622 Europe PMC: 27399966 |
5,057 individuals | East Asian | NR |
GWAS Catalog: GCST003622 Europe PMC: 27399966 |
10,995 individuals | European | NR |
GWAS Catalog: GCST002463 Europe PMC: 24871463 |
3,163 individuals | European | NR |
GWAS Catalog: GCST004867 Europe PMC: 19838195 |
9,169 individuals | European | NR |
GWAS Catalog: GCST001795 Europe PMC: 23273568 |
5,050 individuals | East Asian | NR |
GWAS Catalog: GCST000216 Europe PMC: 19165918 |
2,586 individuals | European | NR |
GWAS Catalog: GCST003599 Europe PMC: 26663301 |
5,420 individuals | East Asian | NR |
GWAS Catalog: GCST000142 Europe PMC: 18204446 |
3,037 individuals | European | NR |
GWAS Catalog: GCST005754 Europe PMC: 29494758 |
2,252 individuals | East Asian | NR |
GWAS Catalog: GCST001384 Europe PMC: 22291604 |
4,275 individuals | East Asian | NR |
GWAS Catalog: GCST000507 Europe PMC: 19838193 |
2,252 individuals | East Asian | NR |
GWAS Catalog: GCST003620 Europe PMC: 27193031 |
16,546 individuals | European | NR |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PPM021383 | PSS011718| Multi-ancestry (including European)| 3,945 individuals |
PGP000648 | Cui J et al. Arthritis Rheumatol (2020) |
Reported Trait: Systemic lupus erythematosus | OR: 2.01 [1.83, 2.22] β: 0.7 (0.05) |
AUROC: 0.696 | — | — | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS011718 | Those 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. | — | [ ,
0.0 % Male samples |
— | European, Not reported | European (98%) | NHS, NHS2 | — |
| PSS011718 | All 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. | — | [ ,
9.7 % Male samples |
— | European, Asian unspecified, African unspecified, Not reported | European (68.1%), Asian (4.9%), African (14.2%), Not reported (12.8%) | PHB | — |