Polygenic Score (PGS) ID: PGS001051

Predicted Trait
Reported Trait Polymyalgia rheumatica
Mapped Trait(s) polymyalgia rheumatica (EFO_0008518)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC96
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC96
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 69
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 1,504 cases
  • , 268,200 controls
]
 European UKB — — — white British ancestry —

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.

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
PPM008013 PSS004751|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Polymyalgia rheumatica — AUROC: 0.84007 [0.73377, 0.94637] R²: 0.10995
Incremental AUROC (full-covars): 0.00396
PGS R2 (no covariates): 0.0041
PGS AUROC (no covariates): 0.59347 [0.45814, 0.7288]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008014 PSS004752|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Polymyalgia rheumatica — AUROC: 0.94435 [0.88977, 0.99892] R²: 0.24363
Incremental AUROC (full-covars): 0.00372
PGS R2 (no covariates): 0.00287
PGS AUROC (no covariates): 0.45385 [0.09439, 0.81331]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008015 PSS004753|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Polymyalgia rheumatica — AUROC: 0.82077 [0.78717, 0.85438] R²: 0.12384
Incremental AUROC (full-covars): 0.0077
PGS R2 (no covariates): 0.01385
PGS AUROC (no covariates): 0.60167 [0.54507, 0.65826]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008016 PSS004754|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Polymyalgia rheumatica — AUROC: 0.73708 [0.62459, 0.84956] R²: 0.05254
Incremental AUROC (full-covars): 0.00266
PGS R2 (no covariates): 0.00471
PGS AUROC (no covariates): 0.54813 [0.38601, 0.71025]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008017 PSS004755|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Polymyalgia rheumatica — AUROC: 0.76042 [0.73986, 0.78098] R²: 0.07774
Incremental AUROC (full-covars): 0.0165
PGS R2 (no covariates): 0.01265
PGS AUROC (no covariates): 0.61026 [0.58102, 0.6395]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

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
PSS004751 — —
[
  • 13 cases
  • , 6,484 controls
]
 — African unspecified — UKB —
PSS004752 — —
[
  • 3 cases
  • , 1,701 controls
]
 — East Asian — UKB —
PSS004753 — —
[
  • 118 cases
  • , 24,787 controls
]
 — European non-white British ancestry UKB —
PSS004754 — —
[
  • 16 cases
  • , 7,815 controls
]
 — South Asian — UKB —
PSS004755 — —
[
  • 394 cases
  • , 67,031 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)