Trait: merkel cell virus seropositivity

Experimental Factor Ontology (EFO) Information
Identifier EFO_0010906
Description The result of a measurement of circulating merkel cell virus-specific antibodies.
Trait category
Other measurement
Synonym MKV 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)
PGS000977
(GBE_BIN23067)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 MCV seropositivity for Merkel Cell Polyomavirus merkel cell virus seropositivity 3
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000977/ScoringFiles/PGS000977.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
PPM007678 PGS000977
(GBE_BIN23067)
 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 PGS000977
(GBE_BIN23067)
 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 PGS000977
(GBE_BIN23067)
 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 PGS000977
(GBE_BIN23067)
 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 PGS000977
(GBE_BIN23067)
 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)