Polygenic Score (PGS) ID: PGS000813

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS Catalog: July 2, 2021
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Score Details

Score Construction
PGS Name PRS46_melanoma
Development Method
Name SNPs significantly associated with melanoma
Parameters Fine mapping of GWAS loci to identify a subset of SNPs which have been repeatedly reported and validated in independent analyses.
Variants
Original Genome Build NR
Number of Variants 46
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000197
Citation (link to publication) Potjer TP et al. J Med Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
36,077 individuals (100%)
PGS Evaluation
European: 100%
1 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 10 cohorts
  • AMFS
  • ,Essen-Heidelberg
  • ,GenoMEL
  • ,Harvard
  • ,LMC
  • ,MDACCS
  • ,MELARISK
  • ,Q-MEGA
  • ,SEARCH
  • ,WAMHS

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
PPM002147 PSS001053|
European Ancestry|
3,841 individuals
 PGP000197 |
Potjer TP et al. J Med Genet (2020)
 Reported Trait: Familial cutaneous melanoma in non-carriers of a CDKN2A mutation OR: 2.12 [1.9, 2.35] AUROC: 0.77 [0.75, 0.79] Odds ratio (OR, top 10% vs. middle 20%): 5.7 [3.93, 8.28] Age, sex —
PPM002148 PSS001053|
European Ancestry|
3,841 individuals
 PGP000197 |
Potjer TP et al. J Med Genet (2020)
 Reported Trait: Single familial cutaneous melanoma in non-carriers of a CDKN2A mutation OR: 1.98 [1.77, 2.22] — — Age, sex —
PPM002149 PSS001053|
European Ancestry|
3,841 individuals
 PGP000197 |
Potjer TP et al. J Med Genet (2020)
 Reported Trait: Multiple familial cutaneous melanoma in non-carriers of a CDKN2A mutation OR: 2.86 [2.3, 3.55] — — Age, sex —

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
PSS001053 Cases are individuals with cutaneous melanoma with at least one other relative (up to third-degree) with cutaneous melanoma and that do not carry a previously identified germline mutation in the CDKN2A gene. Of the cases, 338 were single melanoma and 80 were multiple primary melanoma. —
[
  • 418 cases
  • , 3,423 controls
]
,
44.88 % Male samples
 Mean = 55.91 years European
(Dutch)		 — NBS Cases were recruited from Clinical Genetic Centres throughout the Netherlands.