| Predicted Trait | |
| Reported Trait | Spondyloarthroparthy |
| Mapped Trait(s) | spondyloarthropathy (EFO_0000706) |
| Score Construction | |
| PGS Name | G-PROB_SpA |
| 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 | 31 |
| 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: 90.5% East Asian: 9.5% 32,957 individuals (100%) |
| PGS Evaluation | |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST005529 Europe PMC: 23749187 |
22,647 individuals | European | NR |
GWAS Catalog: GCST005529 Europe PMC: 23749187 |
3,117 individuals | East Asian | NR |
GWAS Catalog: GCST000563 Europe PMC: 20062062 |
7,193 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 |
|---|---|---|---|---|---|---|---|---|
| PPM000580 | PSS000317| European Ancestry| 243 individuals |
PGP000081 | Knevel R et al. Sci Transl Med (2020) |
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis | — | AUROC: 0.56 [0.33, 0.84] | — | — | (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit) |
| PPM000574 | PSS000316| European Ancestry| 245 individuals |
PGP000081 | Knevel R et al. Sci Transl Med (2020) |
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis | — | AUROC: 0.87 [0.76, 0.96] | — | — | (Setting II: Assigning patient diagnoses based on medical records) |
| PPM000568 | PSS000323| Multi-ancestry (including European)| 1,211 individuals |
PGP000081 | Knevel R et al. Sci Transl Med (2020) |
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis | — | AUROC: 0.58 [0.5, 0.67] | — | — | (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 |
|---|---|---|---|---|---|---|---|---|
| PSS000323 | 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 | — |
| PSS000316 | 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 | — |
| PSS000317 | 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 | — |