Polygenic Score (PGS) ID: PGS000462

Predicted Trait
Reported Trait Squamous cell carcinoma
Mapped Trait(s) squamous cell carcinoma (EFO_0000707)
Additional Trait Information PheCode 172.22
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_UKB_20200608
Variants
Original Genome Build GRCh37
Number of Variants 13
Development Method
Name GWAS Hits
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
362,144 individuals (100%)
Score Development/Training
European: 100%
61,038 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003327
Europe PMC: 26829030
61,457 individuals European
GWAS Catalog: GCST003422
Europe PMC: 26908436
13,550 individuals European
GWAS Catalog: GCST003655
Europe PMC: 27424798
287,137 individuals European
Score Development/Training
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
PheCode:172.22; ICD9:173, 173.0, 173.1, 173.2, 173.3, 173.4, 173.5, 173.6, 173.7, 173.8, 173.9; ICD10:C44.0, C44.1, C44.2, C44.3, C44.4, C44.5, C44.6, C44.7, C44.8, C44.9
[
  • 5,550 cases
  • , 55,488 controls
]
European UKB

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
PPM001147 PSS000569|
European Ancestry|
60,018 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Squamous cell carcinoma OR: 1.324 [1.288, 1.361]
β: 0.28 (0.014)
AUROC: 0.573 [0.564, 0.58] Nagelkerke's Pseudo-R²: 0.0141
Brier score: 0.082
Odds Ratio (OR, top 1% vs. Rest): 2.13 [1.74, 2.61]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_UKB_20200608

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
PSS000569 PheCode:172.22; ICD9:173, 173.0, 173.1, 173.2, 173.3, 173.4, 173.5, 173.6, 173.7, 173.8, 173.9; ICD10:C44.0, C44.1, C44.2, C44.3, C44.4, C44.5, C44.6, C44.7, C44.8, C44.9
[
  • 5,450 cases
  • , 54,568 controls
]
European UKB