Polygenic Score (PGS) ID: PGS001131

Predicted Trait
Reported Trait Zoster [herpes zoster] (time-to-event)
Mapped Trait(s) Herpes Zoster (EFO_0006510)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC530
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_HC530
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 82
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
—
[
  • 8,890 cases
  • , 260,814 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
PPM008383 PSS004516|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE zoster [herpes zoster] — AUROC: 0.66564 [0.59848, 0.7328] R²: 0.02855
Incremental AUROC (full-covars): 0.00653
PGS R2 (no covariates): 0.00463
PGS AUROC (no covariates): 0.5717 [0.50786, 0.63553]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008384 PSS004517|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE zoster [herpes zoster] — AUROC: 0.6496 [0.5711, 0.7281] R²: 0.02884
Incremental AUROC (full-covars): 0.00319
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.49296 [0.39896, 0.58695]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008385 PSS004518|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE zoster [herpes zoster] — AUROC: 0.61339 [0.59385, 0.63293] R²: 0.01934
Incremental AUROC (full-covars): 0.00397
PGS R2 (no covariates): 0.00108
PGS AUROC (no covariates): 0.52734 [0.50543, 0.54926]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008386 PSS004519|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE zoster [herpes zoster] — AUROC: 0.64482 [0.60407, 0.68558] R²: 0.02792
Incremental AUROC (full-covars): -0.00388
PGS R2 (no covariates): 0.00012
PGS AUROC (no covariates): 0.49268 [0.44738, 0.53799]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008387 PSS004520|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE zoster [herpes zoster] — AUROC: 0.60947 [0.59775, 0.62119] R²: 0.0198
Incremental AUROC (full-covars): 0.00787
PGS R2 (no covariates): 0.00329
PGS AUROC (no covariates): 0.54558 [0.53361, 0.55755]		 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
PSS004516 — —
[
  • 63 cases
  • , 6,434 controls
]
 — African unspecified — UKB —
PSS004517 — —
[
  • 38 cases
  • , 1,666 controls
]
 — East Asian — UKB —
PSS004518 — —
[
  • 690 cases
  • , 24,215 controls
]
 — European non-white British ancestry UKB —
PSS004519 — —
[
  • 148 cases
  • , 7,683 controls
]
 — South Asian — UKB —
PSS004520 — —
[
  • 2,222 cases
  • , 65,203 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)