Polygenic Score (PGS) ID: PGS000976

Predicted Trait
Reported Trait JCV seropositivity for Human Polyomavirus JCV
Mapped Trait(s) polyomavirus 2 seropositivity (EFO_0010907)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN23066
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_BIN23066
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 16
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%
5,368 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
—
[
  • 3,041 cases
  • , 2,327 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
PPM007673 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 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 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 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 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)