Polygenic Score (PGS) ID: PGS000731

Predicted Trait
Reported Trait Squamous cell carcinoma
Mapped Trait(s) squamous cell carcinoma (EFO_0000707)
Released in PGS Catalog: Feb. 23, 2021
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Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
Development Method
Name RiskPipe (clumping and thresholding)
Parameters p<1e-6
Original Genome Build hg19
Number of Variants 14
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000138
Citation (link to publication) Fontanillas P et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
103,008 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 33420020
  • 7,479 cases
  • , 95,529 controls
42.6 % Male samples
European 23andMe

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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM001671 PSS000873|
European Ancestry|
88,924 individuals
PGP000138 |
Fontanillas P et al. Nat Commun (2021)
Reported Trait: Squamous cell carcinoma OR: 1.44 [1.41, 1.48] AUROC: 0.605

Evaluated Samples

PGS Sample Set ID
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
PSS000873 Squamous cell carcinoma cases were determined by a baseline survey containing 34 questions regarding personal history of skin cancer(including skin cancer type, age at diagnosis, body location, prescribed treatments and information regarding cancer recurrence)
  • 7,914 cases
  • , 81,010 controls
38.9 % Male samples
European 23andMe