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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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

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 SN... Ps with MAF deviation >15% between GWAS Catalog and MGI. GWAS Study identifiers were not listed.Show more
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
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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
EuropeanMGIBasal cell carcinoma: ICD9-173.01,173.11,173.21,173.31,173.41,173.51,173.61,173.71,173.81,173.91Mean = 54.2 years
Sd = 15.9 years		———
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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.

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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
PPM000341PSS000209|
European Ancestry|
20,468 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Basal cell carcinomaOR: 1.65 [1.56, 1.75]AUROC: 0.64 [0.62, 0.66]—age, sex, batch, PC1-4—
PPM000344PSS000207|
European Ancestry|
20,468 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Skin cancerOR: 1.32 [1.27, 1.36]AUROC: 0.58 [0.56, 0.58]—age, sex, batch, PC1-4—
PPM000347PSS000211|
European Ancestry|
149,857 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Skin cancerOR: 1.4 [1.42, 1.48]——age, sex, genotyping array, first 4 genotype PCs—
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Evaluated Samples

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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
PSS000207PheCode 172—
[
  • 3,002 cases
  • , 17,466 controls
]
,
46.9 % Male samples
Mean = 54.2 years
Sd = 15.9 years		European—MGI—
PSS000209Basal 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—
PSS000211PheCode 172—
[
  • 13,624 cases
  • , 136,233 controls
]
,
45.9 % Male samples
Mean = 57.7 years
Sd = 8.1 years		EuropeanWhite British SubsetUKB—
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