Lupus & antiphospholipid syndrome
Phenotype Risk Score but Not Genetic Risk Score Aids in Identifying Individuals With Systemic Lupus Erythematosus in the Electronic Health Record
Authors' conclusion
We developed a SLE PheRS to identify established and undiagnosed SLE individuals. A SLE GRS using known risk SNPs did not add value beyond the PheRS and was of limited utility in Black individuals with SLE.
Study context
- Population
- Individuals in a de-identified electronic health record (EHR) database with an associated DNA biobank
- Participants
- 789 vs 2,261
- Comparison
- Systemic lupus erythematosus (SLE) cases vs controls; Phenotype risk score (PheRS) alone vs PheRS plus genetic risk score (GRS) for identifying SLE
- SLE casesn = 789
- Controlsn = 2,261reference
- Outcome
- Utility of a phenotype risk score (PheRS) and a genetic risk score (GRS) to identify SLE individuals
Methodological detailsde-identified EHR database with associated DNA biobank, PheRS developed using billing codes capturing ACR SLE criteria; GRS with 58 SLE risk single-nucleotide polymorphisms (SNPs)
- De-identified EHR database with associated DNA biobank
- PheRS developed using billing codes capturing ACR SLE criteria; GRS with 58 SLE risk SNPs
Main finding
As reported in the abstract
PheRS
SLE cases
7.7
mean · SD 8.0
Controls
0.8
mean · SD 2.0
P < 0.001
- Model using only PheRS, AUC
- 0.87
- Model adding GRS to PheRS, AUC (minimal difference)
- 0.89
Observational data: associations, not effects.
Further findings
Mean
| Outcome | SLE cases | Controls | P value |
|---|---|---|---|
| GRS | 12.2 (SD 2.3) | 11.0 (SD 2.0) | P < 0.001 |
| PheRS in SLE cases, Black vs White individuals (subgroup) | P = 0.002 | ||
| GRS in SLE cases, Black vs White individuals (subgroup) | P < 0.001 |
- PheRS in SLE cases, Black vs White individuals (subgroup): Black mean 10.0 (SD 10.1)
- PheRS in SLE cases, Black vs White individuals (subgroup): White mean 7.1 (SD 7.2)
- GRS in SLE cases, Black vs White individuals (subgroup): Black mean 9.0 (SD 1.4)
- GRS in SLE cases, Black vs White individuals (subgroup): White mean 12.3 (SD 1.7)
Chart review of controls
- Controls with the highest PheRS and GRS had undiagnosed SLE
Original publication
Phenotype Risk Score but Not Genetic Risk Score Aids in Identifying Individuals With Systemic Lupus Erythematosus in the Electronic Health Record. Arthritis Rheumatol. Published 12 July 2023. doi:10.
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