Polygenic Score (PGS) ID: PGS000119

Predicted Trait
Reported Trait Basal cell carcinoma
Mapped Trait(s) basal cell carcinoma (EFO_0004193)
Released in PGS Catalog: March 27, 2020
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Score Details

Score Construction
PGS Name BCC32
Development Method
Name GWAS Catalog SNPs
Parameters SNPs discovered from GWAS studies with broad European ancestry, LD pruned (r2 > 0.1), filtered SNPs with MAF deviation >15% between GWAS Catalog and MGI. GWAS Study identifiers were not listed.
Variants
Original Genome Build GRCh37
Number of Variants 32
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000055
Citation (link to publication) Fritsche LG et al. PLoS Genet (2019)
Ancestry Distribution
Score Development/Training
European: 100%
10,234 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

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
—
[
  • 419 cases
  • , 9,815 controls
]
,
46.9 % Male samples
 European MGI Basal cell carcinoma: ICD9-173.01,173.11,173.21,173.31,173.41,173.51,173.61,173.71,173.81,173.91 Mean = 54.2 years
Sd = 15.9 years		 — — —

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
PPM000344 PSS000207|
European Ancestry|
20,468 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Skin cancer OR: 1.32 [1.27, 1.36] AUROC: 0.58 [0.56, 0.58] — age, sex, batch, PC1-4 —
PPM000341 PSS000209|
European Ancestry|
20,468 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Basal cell carcinoma OR: 1.65 [1.56, 1.75] AUROC: 0.64 [0.62, 0.66] — age, sex, batch, PC1-4 —
PPM000347 PSS000211|
European Ancestry|
149,857 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Skin cancer OR: 1.4 [1.42, 1.48] — — age, sex, genotyping array, first 4 genotype PCs —

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
PSS000207 PheCode 172 —
[
  • 3,002 cases
  • , 17,466 controls
]
,
46.9 % Male samples
 Mean = 54.2 years
Sd = 15.9 years		 European — MGI —
PSS000209 Basal cell carcinoma: ICD9-173.01,173.11,173.21,173.31,173.41,173.51,173.61,173.71,173.81,173.91 —
[
  • 884 cases
  • , 19,584 controls
]
,
46.9 % Male samples
 Mean = 54.2 years
Sd = 15.9 years		 European — MGI —
PSS000211 PheCode 172 —
[
  • 13,624 cases
  • , 136,233 controls
]
,
45.9 % Male samples
 Mean = 57.7 years
Sd = 8.1 years		 European White British Subset UKB —