Polygenic Score (PGS) ID: PGS000730

Predicted Trait
Reported Trait Basal cell carcinoma
Mapped Trait(s) basal cell carcinoma (EFO_0004193)
Released in PGS Catalog: Feb. 23, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name PRS_BCC
Development Method
Name RiskPipe (clumping and thresholding)
Parameters p<1e-6
Variants
Original Genome Build hg19
Number of Variants 47
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
[
  • 14,898 cases
  • , 88,110 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
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM001670 PSS000871|
European Ancestry|
88,924 individuals
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Reported Trait: Basal cell carcinoma OR: 1.57 [1.55, 1.6] AUROC: 0.624 — — —

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
PSS000871 Basal 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) —
[
  • 16,184 cases
  • , 72,740 controls
]
,
38.9 % Male samples
 European — 23andMe —