Trait: common wart

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009662
Description A wart caused by human papillomavirus. It can appear anywhere on the skin. [NCIT: C27087]
Trait category
Cancer
Synonyms 6 synonyms
  • common wart
  • verruca vulgaris
  • viral Warts
  • viral Warts due to papilloma virus
  • viral wart
  • wart
Mapped terms 12 mapped terms
  • DOID:11165
  • ICD10:B07
  • ICD10:B07.8
  • ICD9:078.1
  • ICD9:078.10
  • ICD9:078.19
  • MESH:D014860
  • MONDO:0001209
  • NCIT:C27087
  • SCTID:57019003
  • UMLS:C0043037
  • UMLS:C3665596

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)
PGS001011
(GBE_HC534)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Viral warts (time-to-event) common wart 5
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001011/ScoringFiles/PGS001011.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
PPM007818 PGS001011
(GBE_HC534)
 PSS004521|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.62763 [0.56904, 0.68622] R²: 0.01913
Incremental AUROC (full-covars): -0.00455
PGS R2 (no covariates): 0.00116
PGS AUROC (no covariates): 0.48242 [0.41987, 0.54497]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007819 PGS001011
(GBE_HC534)
 PSS004522|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.65545 [0.57671, 0.73418] R²: 0.03677
Incremental AUROC (full-covars): -0.00026
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.50846 [0.40705, 0.60986]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007820 PGS001011
(GBE_HC534)
 PSS004523|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.56023 [0.54032, 0.58015] R²: 0.0051
Incremental AUROC (full-covars): 0.01103
PGS R2 (no covariates): 0.00154
PGS AUROC (no covariates): 0.53437 [0.51402, 0.55472]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007821 PGS001011
(GBE_HC534)
 PSS004524|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.5793 [0.54592, 0.61268] R²: 0.01114
Incremental AUROC (full-covars): 0.00245
PGS R2 (no covariates): 0.00048
PGS AUROC (no covariates): 0.51036 [0.47743, 0.54328]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007822 PGS001011
(GBE_HC534)
 PSS004525|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.56004 [0.54811, 0.57198] R²: 0.00576
Incremental AUROC (full-covars): 0.00636
PGS R2 (no covariates): 0.00167
PGS AUROC (no covariates): 0.53057 [0.51862, 0.54252]		 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
PSS004521 — —
[
  • 81 cases
  • , 6,416 controls
]
 — African unspecified — UKB —
PSS004522 — —
[
  • 32 cases
  • , 1,672 controls
]
 — East Asian — UKB —
PSS004523 — —
[
  • 781 cases
  • , 24,124 controls
]
 — European non-white British ancestry UKB —
PSS004524 — —
[
  • 307 cases
  • , 7,524 controls
]
 — South Asian — UKB —
PSS004525 — —
[
  • 2,358 cases
  • , 65,067 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)