PGS Publication: PGP000197

Publication Information (EuropePMC)
Title Association between a 46-SNP Polygenic Risk Score and melanoma risk in Dutch patients with familial melanoma.
PubMed ID 32994281(Europe PMC)
doi 10.1136/jmedgenet-2020-107251
Publication Date Sept. 29, 2020
Journal J Med Genet
Author(s) Potjer TP, van der Grinten TWJ, Lakeman IMM, Bollen SH, Rodríguez-Girondo M, Iles MM, Barrett JH, Kiemeney LA, Gruis NA, van Asperen CJ, van der Stoep N.
Released in PGS Catalog: July 2, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000813
(PRS46_melanoma)
 PGP000197 |
Potjer TP et al. J Med Genet (2020)
 Melanoma melanoma 46
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000813/ScoringFiles/PGS000813.txt.gz

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) 		Evaluated Score 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 PGS000813
(PRS46_melanoma)
 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 PGS000813
(PRS46_melanoma)
 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 PGS000813
(PRS46_melanoma)
 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.