Trait: polyomavirus 2 seropositivity

Experimental Factor Ontology (EFO) Information
Identifier EFO_0010907
Description The result of a measurement of circulating polyomavirus 2-specific antibodies.
Trait category
Other measurement
Synonym JCV seropositivity
Mapped term PMID:33204752

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)
PGS000976
(GBE_BIN23066)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 JCV seropositivity for Human Polyomavirus JCV polyomavirus 2 seropositivity 16
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000976/ScoringFiles/PGS000976.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
PPM007673 PGS000976
(GBE_BIN23066)
 PSS003681|
African Ancestry|
119 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: JCV seropositivity for Human Polyomavirus JCV — AUROC: 0.68909 [0.58955, 0.78863] R²: 0.1586
Incremental AUROC (full-covars): 0.00736
PGS R2 (no covariates): 0.02381
PGS AUROC (no covariates): 0.57396 [0.46002, 0.6879]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007674 PGS000976
(GBE_BIN23066)
 PSS003682|
East Asian Ancestry|
41 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: JCV seropositivity for Human Polyomavirus JCV — AUROC: 0.80208 [0.65148, 0.95269] R²: 0.38151
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.0442
PGS AUROC (no covariates): 0.56944 [0.30952, 0.82937]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007675 PGS000976
(GBE_BIN23066)
 PSS003683|
European Ancestry|
471 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: JCV seropositivity for Human Polyomavirus JCV — AUROC: 0.64245 [0.59174, 0.69316] PGS R2 (no covariates): 0.02805
R²: 0.07596
Incremental AUROC (full-covars): 0.05216
PGS AUROC (no covariates): 0.59653 [0.54396, 0.64911]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007676 PGS000976
(GBE_BIN23066)
 PSS003684|
South Asian Ancestry|
164 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: JCV seropositivity for Human Polyomavirus JCV — AUROC: 0.70304 [0.60641, 0.79967] R²: 0.17879
Incremental AUROC (full-covars): 0.01418
PGS R2 (no covariates): 0.03568
PGS AUROC (no covariates): 0.59211 [0.4918, 0.69241]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007677 PGS000976
(GBE_BIN23066)
 PSS003685|
European Ancestry|
1,275 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: JCV seropositivity for Human Polyomavirus JCV — AUROC: 0.62177 [0.59085, 0.65268] R²: 0.06064
Incremental AUROC (full-covars): 0.07692
PGS R2 (no covariates): 0.05929
PGS AUROC (no covariates): 0.62071 [0.58991, 0.65151]		 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
PSS003681 — —
[
  • 83 cases
  • , 36 controls
]
 — African unspecified — UKB —
PSS003682 — —
[
  • 32 cases
  • , 9 controls
]
 — East Asian — UKB —
PSS003683 — —
[
  • 295 cases
  • , 176 controls
]
 — European non-white British ancestry UKB —
PSS003684 — —
[
  • 117 cases
  • , 47 controls
]
 — South Asian — UKB —
PSS003685 — —
[
  • 722 cases
  • , 553 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)