Polygenic Score (PGS) ID: PGS003382

Predicted Trait
Reported Trait Skin cutaneous melanoma
Mapped Trait(s) cutaneous melanoma (EFO_0000389)
Released in PGS Catalog: Jan. 19, 2023
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Score Details

Score Construction
PGS Name best_SKCM
Development Method
Name Pruning and Thresholding (P+T)
Parameters p < 1×10^-4, r2 < 0.1
Variants
Original Genome Build GRCh37
Number of Variants 672
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000413
Citation (link to publication) Namba S et al. Cancer Res (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
111,549 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 30,134 cases
  • , 81,415 controls
]
 European NR

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
PPM016257 PSS010085|
European Ancestry|
273,786 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: skin cutaneous melanoma — AUROC: 0.682 R²: 0.0261 age, sex, top 20 genetic principal components —

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
PSS010085 C43 —
[
  • 4,242 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer