Polygenic Score (PGS) ID: PGS000744

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Additional Trait Information Genes involved in the pigment pathway
Released in PGS Catalog: March 22, 2021
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Score Details

Score Construction
PGS Name PRS_melanoma_pigment.pathway
Development Method
Name Genome-wide significant variants
Parameters SNPs with previously confirmed melanoma risk in genes involved in the pigmentation pathway
Variants
Original Genome Build NR
Number of Variants 31
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000151
Citation (link to publication) Cust AE et al. J Invest Dermatol (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
36,077 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003061
Europe PMC: 26237428
 36,077 individuals 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
PPM001830 PSS000927|
European Ancestry|
1,035 individuals
 PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
 Reported Trait: Melanoma OR: 1.71 [1.49, 1.96] — Odds Ratio (OR, top vs. bottom tertile): 3.11 [2.21, 4.36]
Odds Ratio (OR, top vs. bottom decile): 5.75 [3.09, 10.72]		 Age, sex, recruitment city, self-reported European ancestry —
PPM001831 PSS000928|
European Ancestry|
1,460 individuals
 PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
 Reported Trait: Melanoma OR: 1.66 [1.49, 1.86] — Odds Ratio (OR, top vs. bottom tertile): 2.94 [2.23, 3.88]
Odds Ratio (OR, top vs. bottom decile): 7.0 [4.12, 11.88]		 Age, sex, self reported European ancestry —

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
PSS000927 Cases include invasive cutaneous melanoma diagnoses between ages 18 and 39 years —
[
  • 578 cases
  • , 457 controls
]
,
40.0 % Male samples
 — European — AMFS —
PSS000928 Cases include histopathologically confirmed invasive melanoma cases in patients between 18 and 82 years. —
[
  • 964 cases
  • , 496 controls
]
,
40.0 % Male samples
 — European — LMC —