Polygenic Score (PGS) ID: PGS000407

Predicted Trait
Reported Trait Skin cancer
Mapped Trait(s) skin carcinoma (EFO_0009259)
Additional Trait Information PheCode 172
Released in PGS Catalog: Dec. 15, 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 PRSWEB_PHECODE172_UKBB-SAIGE-HRC-X172_LASSOSUM_MGI_20200608
Development Method
Name lassosum
Parameters s=0.2;Lambda=0.01438
Variants
Original Genome Build GRCh37
Number of Variants 3,166
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%
408,823 individuals (100%)
Score Development/Training
European: 100%
17,370 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
[
  • 13,752 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
[
  • 3,542 cases
  • , 13,828 controls
]
 European MGI PheCode:172; ICD9CM:172.0, 172.1, 172.2, 172.3, 172.4, 172.5, 172.6, 172.7, 172.8, 172.9, 173.00, 173.01, 173.02, 173.09, 173.10, 173.11, 173.12, 173.19, 173.20, 173.21, 173.22, 173.29, 173.30, 173.31, 173.32, 173.39, 173.40, 173.41, 173.42, 173.49, 173.50, 173.51, 173.52, 173.59, 173.60, 173.61, 173.62, 173.69, 173.70, 173.71, 173.72, 173.79, 173.80, 173.81, 173.82, 173.89, 173.90, 173.91, 173.92, 173.99, 209.31, 209.32, 209.33, 209.34, 209.35, 209.36, 232.0, 232.1, 232.2, 232.3, 232.4, 232.5, 232.6, 232.7, 232.8, 232.9, V10.82, V10.83; ICD10CM:C43, C43.0, C43.1, C43.10, C43.11, C43.12, C43.2, C43.20, C43.21, C43.22, C43.3, C43.30, C43.31, C43.39, C43.4, C43.5, C43.51, C43.52, C43.59, C43.6, C43.60, C43.61, C43.62, C43.7, C43.70, C43.71, C43.72, C43.8, C43.9, C44.0, C44.00, C44.01, C44.02, C44.09, C44.1, C44.10, C44.101, C44.102, C44.109, C44.11, C44.111, C44.112, C44.119, C44.12, C44.121, C44.122, C44.129, C44.19, C44.191, C44.192, C44.199, C44.2, C44.20, C44.201, C44.202, C44.209, C44.21, C44.211, C44.212, C44.219, C44.22, C44.221, C44.222, C44.229, C44.29, C44.291, C44.292, C44.299, C44.30, C44.300, C44.301, C44.309, C44.31, C44.310, C44.311, C44.319, C44.320, C44.321, C44.329, C44.39, C44.390, C44.391, C44.399, C44.4, C44.40, C44.41, C44.42, C44.49, C44.500, C44.501, C44.509, C44.51, C44.510, C44.511, C44.519, C44.52, C44.520, C44.521, C44.529, C44.59, C44.590, C44.591, C44.599, C44.6, C44.60, C44.601, C44.602, C44.609, C44.61, C44.611, C44.612, C44.619, C44.62, C44.621, C44.622, C44.629, C44.69, C44.691, C44.692, C44.699, C44.7, C44.70, C44.701, C44.702, C44.709, C44.71, C44.711, C44.712, C44.719, C44.72, C44.721, C44.722, C44.729, C44.79, C44.791, C44.792, C44.799, C44.8, C44.80, C44.81, C44.82, C44.89, C44.9, C44.90, C44.91, C44.92, C44.99, C4A, C4A.0, C4A.1, C4A.10, C4A.11, C4A.12, C4A.2, C4A.20, C4A.21, C4A.22, C4A.3, C4A.30, C4A.31, C4A.39, C4A.4, C4A.5, C4A.51, C4A.52, C4A.59, C4A.6, C4A.60, C4A.61, C4A.62, C4A.7, C4A.70, C4A.71, C4A.72, C4A.8, C4A.9, D03, D03.0, D03.1, D03.10, D03.11, D03.12, D03.2, D03.20, D03.21, D03.22, D03.3, D03.30, D03.39, D03.4, D03.5, D03.51, D03.52, D03.59, D03.6, D03.60, D03.61, D03.62, D03.7, D03.70, D03.71, D03.72, D03.8, D03.9, 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
PPM001092 PSS000548|
European Ancestry|
17,607 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Skin cancer OR: 1.38 [1.328, 1.434]
β: 0.322 (0.0197)		 AUROC: 0.586 [0.575, 0.597] Nagelkerke's Pseudo-R²: 0.0245
Brier score: 0.146
Odds Ratio (OR, top 1% vs. Rest): 2.26 [1.69, 3.03]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172_UKBB-SAIGE-HRC-X172_LASSOSUM_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
PSS000548 PheCode:172; ICD9CM:172.0, 172.1, 172.2, 172.3, 172.4, 172.5, 172.6, 172.7, 172.8, 172.9, 173.00, 173.01, 173.02, 173.09, 173.10, 173.11, 173.12, 173.19, 173.20, 173.21, 173.22, 173.29, 173.30, 173.31, 173.32, 173.39, 173.40, 173.41, 173.42, 173.49, 173.50, 173.51, 173.52, 173.59, 173.60, 173.61, 173.62, 173.69, 173.70, 173.71, 173.72, 173.79, 173.80, 173.81, 173.82, 173.89, 173.90, 173.91, 173.92, 173.99, 209.31, 209.32, 209.33, 209.34, 209.35, 209.36, 232.0, 232.1, 232.2, 232.3, 232.4, 232.5, 232.6, 232.7, 232.8, 232.9, V10.82, V10.83; ICD10CM:C43, C43.0, C43.1, C43.10, C43.11, C43.12, C43.2, C43.20, C43.21, C43.22, C43.3, C43.30, C43.31, C43.39, C43.4, C43.5, C43.51, C43.52, C43.59, C43.6, C43.60, C43.61, C43.62, C43.7, C43.70, C43.71, C43.72, C43.8, C43.9, C44.0, C44.00, C44.01, C44.02, C44.09, C44.1, C44.10, C44.101, C44.102, C44.109, C44.11, C44.111, C44.112, C44.119, C44.12, C44.121, C44.122, C44.129, C44.19, C44.191, C44.192, C44.199, C44.2, C44.20, C44.201, C44.202, C44.209, C44.21, C44.211, C44.212, C44.219, C44.22, C44.221, C44.222, C44.229, C44.29, C44.291, C44.292, C44.299, C44.30, C44.300, C44.301, C44.309, C44.31, C44.310, C44.311, C44.319, C44.320, C44.321, C44.329, C44.39, C44.390, C44.391, C44.399, C44.4, C44.40, C44.41, C44.42, C44.49, C44.500, C44.501, C44.509, C44.51, C44.510, C44.511, C44.519, C44.52, C44.520, C44.521, C44.529, C44.59, C44.590, C44.591, C44.599, C44.6, C44.60, C44.601, C44.602, C44.609, C44.61, C44.611, C44.612, C44.619, C44.62, C44.621, C44.622, C44.629, C44.69, C44.691, C44.692, C44.699, C44.7, C44.70, C44.701, C44.702, C44.709, C44.71, C44.711, C44.712, C44.719, C44.72, C44.721, C44.722, C44.729, C44.79, C44.791, C44.792, C44.799, C44.8, C44.80, C44.81, C44.82, C44.89, C44.9, C44.90, C44.91, C44.92, C44.99, C4A, C4A.0, C4A.1, C4A.10, C4A.11, C4A.12, C4A.2, C4A.20, C4A.21, C4A.22, C4A.3, C4A.30, C4A.31, C4A.39, C4A.4, C4A.5, C4A.51, C4A.52, C4A.59, C4A.6, C4A.60, C4A.61, C4A.62, C4A.7, C4A.70, C4A.71, C4A.72, C4A.8, C4A.9, D03, D03.0, D03.1, D03.10, D03.11, D03.12, D03.2, D03.20, D03.21, D03.22, D03.3, D03.30, D03.39, D03.4, D03.5, D03.51, D03.52, D03.59, D03.6, D03.60, D03.61, D03.62, D03.7, D03.70, D03.71, D03.72, D03.8, D03.9, 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 —
[
  • 3,557 cases
  • , 14,050 controls
]
 — European — MGI —