Polygenic Score (PGS) ID: PGS000463

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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Terms and Licenses
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 7
Development Method
Name P&T
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=1e-11
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003327
EuropePMC: 26829030
61,457 individuals European
GWAS Catalog: GCST003655
EuropePMC: 27424798
287,137 individuals European
GWAS Catalog: GCST003422
EuropePMC: 26908436
13,550 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; ICD9CM:173.02, 173.12, 173.22, 173.32, 173.42, 173.52, 173.62, 173.72, 173.82, 173.92; ICD10CM:C44.02, C44.121, C44.122, C44.129, C44.221, C44.222, C44.229, C44.320, C44.321, C44.329, C44.42, C44.520, C44.521, C44.529, C44.621, C44.622, C44.629, C44.721, C44.722, C44.729, C44.82, C44.92
[
  • 935 cases
  • , 7,094 controls
]
European MGI

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001148 PSS000545 PGP000118
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Squamous cell carcinoma OR: 1.448 [1.356, 1.546]
β: 0.37 (0.0335)
AUROC: 0.593 [0.573, 0.613] Nagelkerke's Pseudo-R²: 0.0268
Brier score: 0.0977
Odds Ratio (OR, top 1% vs. Rest): 3.74 [2.46, 5.68]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_MGI_20200608

Evaluated Samples

PGS Sample Set ID
(PSS 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
PSS000545 PheCode:172.22; ICD9CM:173.02, 173.12, 173.22, 173.32, 173.42, 173.52, 173.62, 173.72, 173.82, 173.92; ICD10CM:C44.02, C44.121, C44.122, C44.129, C44.221, C44.222, C44.229, C44.320, C44.321, C44.329, C44.42, C44.520, C44.521, C44.529, C44.621, C44.622, C44.629, C44.721, C44.722, C44.729, C44.82, C44.92
[
  • 982 cases
  • , 7,491 controls
]
European MGI