Polygenic Score (PGS) ID: PGS000977

Predicted Trait
Reported Trait MCV seropositivity for Merkel Cell Polyomavirus
Mapped Trait(s) merkel cell virus seropositivity (EFO_0010906)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN23067
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_BIN23067
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3
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
—
[
  • 3,549 cases
  • , 1,819 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
PPM007678 PSS003686|
African Ancestry|
119 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: MCV seropositivity for Merkel Cell Polyomavirus — AUROC: 0.67165 [0.5463, 0.797] R²: 0.17235
Incremental AUROC (full-covars): 0.00317
PGS R2 (no covariates): 0.01753
PGS AUROC (no covariates): 0.55299 [0.41519, 0.69079]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007679 PSS003687|
East Asian Ancestry|
41 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: MCV seropositivity for Merkel Cell Polyomavirus — AUROC: 0.84066 [0.71514, 0.96618] R²: 0.42395
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.02665
PGS AUROC (no covariates): 0.5783 [0.38819, 0.7684]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007680 PSS003688|
European Ancestry|
471 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: MCV seropositivity for Merkel Cell Polyomavirus — AUROC: 0.63825 [0.58242, 0.69408] R²: 0.06391
Incremental AUROC (full-covars): 0.02222
PGS R2 (no covariates): 0.01956
PGS AUROC (no covariates): 0.58896 [0.53103, 0.64689]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007681 PSS003689|
South Asian Ancestry|
164 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: MCV seropositivity for Merkel Cell Polyomavirus — AUROC: 0.65892 [0.5633, 0.75454] PGS R2 (no covariates): 0.00468
R²: 0.13619
Incremental AUROC (full-covars): 0.01508
PGS AUROC (no covariates): 0.56717 [0.47462, 0.65972]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007682 PSS003690|
European Ancestry|
1,275 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: MCV seropositivity for Merkel Cell Polyomavirus — AUROC: 0.57766 [0.54413, 0.61119] R²: 0.02645
Incremental AUROC (full-covars): 0.03387
PGS R2 (no covariates): 0.02491
PGS AUROC (no covariates): 0.56617 [0.53296, 0.59938]		 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
PSS003686 — —
[
  • 96 cases
  • , 23 controls
]
 — African unspecified — UKB —
PSS003687 — —
[
  • 28 cases
  • , 13 controls
]
 — East Asian — UKB —
PSS003688 — —
[
  • 351 cases
  • , 120 controls
]
 — European non-white British ancestry UKB —
PSS003689 — —
[
  • 115 cases
  • , 49 controls
]
 — South Asian — UKB —
PSS003690 — —
[
  • 839 cases
  • , 436 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)