Polygenic Score (PGS) ID: PGS000446

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_20001-1061_PRS-CS_MGI_20200608
Development Method
Name PRS-CS
Parameters Parameters = auto; LD reference (eur)
Variants
Original Genome Build GRCh37
Number of Variants 1,111,490
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%
722,282 individuals (100%)
Score Development/Training
European: 100%
11,734 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 3,441 cases
  • , 357,700 controls
]
 European NR
[
  • 519 cases
  • , 360,622 controls
]
 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
PPM001131 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.291 [1.221, 1.366]
β: 0.256 (0.0286)		 AUROC: 0.575 [0.559, 0.591] Nagelkerke's Pseudo-R²: 0.0139
Brier score: 0.109
Odds Ratio (OR, top 1% vs. Rest): 1.42 [0.871, 2.33]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608
PPM018452 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Skin colour β: -0.02375 — R²: 0.01374 — —
PPM018453 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Freckles β: 0.04205 — R²: 0.02091 — —
PPM018454 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Ease suntan β: -0.0266 — R²: 0.01362 — —
PPM018455 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Ease sunburn β: 0.04289 — R²: 0.01118 — —
PPM018456 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Phototype score β: -0.62656 — R²: 0.03377 — —
PPM018457 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Fitzpatrick scale β: -0.02673 — R²: 0.0294 — —
PPM018458 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Red hair β: 1.77173 — R²: 0.05421
pseudo R²: 0.05421		 — —

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
PSS010980 — — 4,797 individuals — European — NR GCAT
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 —