Trait: Varicella zoster virus seropositivity

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009340
Description The result of a measurement of circulating Varicella zoster virus-specific antibodies
Trait category
Other measurement
Synonym VZV seropositivity
Mapped term PMID:30053915

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
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)
PGS001399
(GBE_INI23002)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 GE / gI antigen for Varicella Zoster Virus Varicella zoster virus seropositivity 5
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001399/ScoringFiles/PGS001399.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
PPM005335 PGS001399
(GBE_INI23002)
 PSS005006|
African Ancestry|
119 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: GE / gI antigen for Varicella Zoster Virus — — R²: 0.10887 [0.09458, 0.12316]
Incremental R2 (full-covars): 0.00938
PGS R2 (no covariates): 0.03579 [0.02693, 0.04466]		 age, sex, UKB array type, Genotype PCs —
PPM005336 PGS001399
(GBE_INI23002)
 PSS005007|
East Asian Ancestry|
41 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: GE / gI antigen for Varicella Zoster Virus — — R²: 0.48217 [0.4481, 0.51625]
Incremental R2 (full-covars): 0.00532
PGS R2 (no covariates): 0.00187 [-0.00222, 0.00595]		 age, sex, UKB array type, Genotype PCs —
PPM005337 PGS001399
(GBE_INI23002)
 PSS005008|
European Ancestry|
471 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: GE / gI antigen for Varicella Zoster Virus — — R²: 0.03066 [0.02645, 0.03488]
Incremental R2 (full-covars): 0.00463
PGS R2 (no covariates): 0.00671 [0.00469, 0.00873]		 age, sex, UKB array type, Genotype PCs —
PPM005338 PGS001399
(GBE_INI23002)
 PSS005009|
South Asian Ancestry|
164 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: GE / gI antigen for Varicella Zoster Virus — — R²: 0.11517 [0.10187, 0.12847]
Incremental R2 (full-covars): 0.00241
PGS R2 (no covariates): 0.00552 [0.00225, 0.0088]		 age, sex, UKB array type, Genotype PCs —
PPM005339 PGS001399
(GBE_INI23002)
 PSS005010|
European Ancestry|
1,275 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: GE / gI antigen for Varicella Zoster Virus — — R²: 0.02709 [0.02467, 0.0295]
Incremental R2 (full-covars): 0.01475
PGS R2 (no covariates): 0.02442 [0.02212, 0.02673]		 age, sex, UKB array type, Genotype PCs —

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
PSS005006 — — 119 individuals — African unspecified — UKB —
PSS005007 — — 41 individuals — East Asian — UKB —
PSS005008 — — 471 individuals — European non-white British ancestry UKB —
PSS005009 — — 164 individuals — South Asian — UKB —
PSS005010 — — 1,275 individuals — European white British ancestry UKB Testing cohort (heldout set)