Polygenic Score (PGS) ID: PGS000470

Predicted Trait
Reported Trait Carcinoma in situ of skin
Mapped Trait(s) skin carcinoma in situ (MONDO_0004641)
Additional Trait Information PheCode 172.3
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-07
Variants
Original Genome Build GRCh37
Number of Variants 5
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%
395,738 individuals (100%)
Score Development/Training
European: 100%
6,005 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 32424355
[
  • 667 cases
  • , 395,071 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
[
  • 630 cases
  • , 5,375 controls
]
 European MGI PheCode:172.3; ICD9CM:232.0, 232.1, 232.2, 232.3, 232.4, 232.5, 232.6, 232.7, 232.8, 232.9; ICD10CM:D04, D04.0, D04.1, D04.10, D04.11, D04.12, D04.2, D04.20, D04.21, D04.22, D04.3, D04.30, D04.39, D04.4, D04.5, D04.6, D04.60, D04.61, D04.62, D04.7, D04.70, D04.71, D04.72, D04.8, D04.9 — — — —

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
PPM001155 PSS000547|
European Ancestry|
5,500 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Carcinoma in situ of skin OR: 1.308 [1.208, 1.417]
β: 0.269 (0.0407)		 AUROC: 0.557 [0.531, 0.582] Nagelkerke's Pseudo-R²: 0.0154
Brier score: 0.093
Odds Ratio (OR, top 1% vs. Rest): 2.45 [1.34, 4.45]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_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
PSS000547 PheCode:172.3; ICD9CM:232.0, 232.1, 232.2, 232.3, 232.4, 232.5, 232.6, 232.7, 232.8, 232.9; ICD10CM:D04, D04.0, D04.1, D04.10, D04.11, D04.12, D04.2, D04.20, D04.21, D04.22, D04.3, D04.30, D04.39, D04.4, D04.5, D04.6, D04.60, D04.61, D04.62, D04.7, D04.70, D04.71, D04.72, D04.8, D04.9 —
[
  • 585 cases
  • , 4,915 controls
]
 — European — MGI —