Trait: keratinocyte carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0010176
Description A skin cancer arising from the keratin-producing cells of the epidermis. The term encompasses both basal cell carcinoma and squamous cell carcinoma.
Trait category
Other trait
Synonym keratinocyte cancer
Mapped term PMID:31174203

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:
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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)
PGS004592
(PRS_KC)
 PGP000571 |
Liyanage UE et al. J Eur Acad Dermatol Venereol (2022)
 Keratinocyte cancer keratinocyte carcinoma 78
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004592/ScoringFiles/PGS004592.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
PPM020722 PGS004592
(PRS_KC)
 PSS011383|
European Ancestry|
998 individuals
 PGP000571 |
Liyanage UE et al. J Eur Acad Dermatol Venereol (2022)
 Reported Trait: Keratinocyte cancer OR: 1.51 [1.3, 1.76] AUROC: 0.74 R²: 0.231 Age, sex, self-reported skin tanning ability, clinical grade of neck elastosis, genotyping batch, first 2 PCs —
PPM020723 PGS004592
(PRS_KC)
 PSS011383|
European Ancestry|
998 individuals
 PGP000571 |
Liyanage UE et al. J Eur Acad Dermatol Venereol (2022)
 Reported Trait: Keratinocyte cancer — — Odds ratio (OR, top PRS quintile vs bottom PRS quintile): 3.45 [2.18, 5.5] Age, sex, self-reported skin tanning ability, clinical grade of neck elastosis, genotyping batch, first 2 PCs —

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
PSS011383 — —
[
  • 432 cases
  • , 566 controls
]
,
44.0 % Male samples
 — European — NSCS —