Trait: varicella zoster infection

Trait Information
Identifier MONDO_0005608
Description A highly contagious viral infection caused by the varicella zoster virus. Clinically, it may be manifested as shingles or chicken pox. [NCIT: C96407]
Trait category
Other trait
Synonyms 2 synonyms
  • Varicella-zoster Virus infection
  • varicella zoster infection
Child trait(s) herpes zoster

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows PGS for child terms of "varicella zoster infection" in the EFO hierarchy.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001131
(GBE_HC530)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Zoster [herpes zoster] (time-to-event) herpes zoster 82
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001131/ScoringFiles/PGS001131.txt.gz

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) 		Evaluated Score 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 PGS001131
(GBE_HC530)
 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 PGS001131
(GBE_HC530)
 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 PGS001131
(GBE_HC530)
 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 PGS001131
(GBE_HC530)
 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 PGS001131
(GBE_HC530)
 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)