| Predicted Trait | |
| Reported Trait | Systemic lupus erythematosus |
| Mapped Trait(s) | systemic lupus erythematosus (MONDO_0007915) |
| 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 | |
| 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 |
|
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) |
|
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 | [ ,
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 | [ ,
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 | [ ,
32.0 % Male samples |
— | European | — | PHB | — |