Polygenic Score (PGS) ID: PGS000458

Predicted Trait
Reported Trait Basal cell carcinoma
Mapped Trait(s) basal cell carcinoma (EFO_0004193)
Additional Trait Information PheCode 172.21
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=2.51e-10
Variants
Original Genome Build GRCh37
Number of Variants 23
Effect Weight Type NR
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%
1,048,484 individuals (100%)
Score Development/Training
European: 100%
11,734 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000318
Europe PMC: 19151717
 30,395 individuals European NR
GWAS Catalog: GCST001124
Europe PMC: 21700618
 8,058 individuals European NR
GWAS Catalog: GCST002331
Europe PMC: 24403052
 113,616 individuals European NR
GWAS Catalog: GCST002842
Europe PMC: 25855136
 270,930 individuals European NR
GWAS Catalog: GCST003726
Europe PMC: 27539887
 287,197 individuals European NR
GWAS Catalog: GCST004113
Europe PMC: 28177523
 304,241 individuals European NR
GWAS Catalog: GCST000249
Europe PMC: 18849993
 34,047 individuals European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 32991828
[
  • 1,507 cases
  • , 10,227 controls
]
 European MGI PheCode:172.21; ICD9CM:173.01, 173.11, 173.21, 173.31, 173.41, 173.51, 173.61, 173.71, 173.81, 173.91; ICD10CM:C44.01, C44.111, C44.112, C44.119, C44.211, C44.212, C44.219, C44.310, C44.311, C44.319, C44.41, C44.510, C44.511, C44.519, C44.611, C44.612, C44.619, C44.711, C44.712, C44.719, C44.81, C44.91 — — — —

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
PPM001143 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.634 [1.542, 1.732]
β: 0.491 (0.0296)		 AUROC: 0.628 [0.612, 0.644] Nagelkerke's Pseudo-R²: 0.0457
Brier score: 0.106
Odds Ratio (OR, top 1% vs. Rest): 4.03 [2.86, 5.69]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_MGI_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
PSS000544 PheCode:172.21; ICD9CM:173.01, 173.11, 173.21, 173.31, 173.41, 173.51, 173.61, 173.71, 173.81, 173.91; ICD10CM:C44.01, C44.111, C44.112, C44.119, C44.211, C44.212, C44.219, C44.310, C44.311, C44.319, C44.41, C44.510, C44.511, C44.519, C44.611, C44.612, C44.619, C44.711, C44.712, C44.719, C44.81, C44.91 —
[
  • 1,481 cases
  • , 9,841 controls
]
 — European — MGI —