Polygenic Score (PGS) ID: PGS000428

Predicted Trait
Reported Trait Melanomas of skin (diagnosis or history)
Mapped Trait(s) melanoma (EFO_0000756)
Additional Trait Information PheCode 172.1
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE172.1_Melanoma-Ransohoff_PT_UKB_20200608
Variants
Original Genome Build GRCh37
Number of Variants 20
Development Method
Name P&T
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=3.5e-08
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%
294,219 individuals (100%)
Score Development/Training
European: 100%
14,991 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
Europe PMC: 28212542
[
  • 6,628 cases
  • , 287,591 controls
]
European
Score Development/Training
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
PheCode:172.1; ICD9:-; ICD10:C43.0, C43.1, C43.2, C43.3, C43.4, C43.5, C43.6, C43.7, C43.8, C43.9, D03.0, D03.1, D03.2, D03.3, D03.4, D03.5, D03.6, D03.7, D03.8, D03.9
[
  • 1,364 cases
  • , 13,627 controls
]
European UKB

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
PPM001113 PSS000567|
European Ancestry|
14,482 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.551 [1.463, 1.643]
β: 0.439 (0.0296)
AUROC: 0.62 [0.604, 0.635] Nagelkerke's Pseudo-R²: 0.0335
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 2.81 [1.93, 4.07]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_Melanoma-Ransohoff_PT_UKB_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
PSS000567 PheCode:172.1; ICD9:-; ICD10:C43.0, C43.1, C43.2, C43.3, C43.4, C43.5, C43.6, C43.7, C43.8, C43.9, D03.0, D03.1, D03.2, D03.3, D03.4, D03.5, D03.6, D03.7, D03.8, D03.9
[
  • 1,317 cases
  • , 13,165 controls
]
European UKB