Polygenic Score (PGS) ID: PGS000118

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS Catalog: March 27, 2020
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Score Details

Score Construction
PGS Name MEL29
Development Method
Name GWAS Catalog SNPs
Parameters SNPs discovered from GWAS studies with broad European ancestry, LD pruned (r2 > 0.1), filtered SNPs with MAF deviation >15% between GWAS Catalog and MGI. GWAS Study identifiers were not listed.
Variants
Original Genome Build GRCh37
Number of Variants 29
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000055
Citation (link to publication) Fritsche LG et al. PLoS Genet (2019)
Ancestry Distribution
Score Development/Training
European: 100%
10,234 individuals (100%)
PGS Evaluation
European: 100%
4 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 617 cases
  • , 9,617 controls
]
,
46.9 % Male samples
 European MGI Melanomas of skin : ICD9- 172.0,172.1,172.2,172.3,172.4,172.5,172.6,172.7,172.8,172.9 Mean = 54.2 years
Sd = 15.9 years		 — — —

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
PPM000339 PSS000206|
European Ancestry|
20,468 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Melanoma OR: 1.48 [1.41, 1.56] AUROC: 0.61 [0.59, 0.62] — age, sex, batch, PC1-4 —
PPM000342 PSS000207|
European Ancestry|
20,468 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Skin cancer OR: 1.3 [1.26, 1.34] AUROC: 0.57 [0.56, 0.58] — age, sex, batch, PC1-4 —
PPM000348 PSS000210|
European Ancestry|
29,898 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Melanoma OR: 1.5 [1.44, 1.55] — — age, sex, genotyping array, first 4 genotype PCs —
PPM000345 PSS000211|
European Ancestry|
149,857 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Skin cancer OR: 1.2 [1.22, 1.36] — — age, sex, genotyping array, first 4 genotype PCs —

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
PSS000206 Melanomas of skin : ICD9- 172.0,172.1,172.2,172.3,172.4,172.5,172.6,172.7,172.8,172.9 —
[
  • 1,279 cases
  • , 19,189 controls
]
,
46.9 % Male samples
 Mean = 54.2 years
Sd = 15.9 years		 European — MGI —
PSS000207 PheCode 172 —
[
  • 3,002 cases
  • , 17,466 controls
]
,
46.9 % Male samples
 Mean = 54.2 years
Sd = 15.9 years		 European — MGI —
PSS000210 PheCode 172.11 —
[
  • 2,718 cases
  • , 27,180 controls
]
,
45.9 % Male samples
 Mean = 57.7 years
Sd = 8.1 years		 European White British Subset UKB —
PSS000211 PheCode 172 —
[
  • 13,624 cases
  • , 136,233 controls
]
,
45.9 % Male samples
 Mean = 57.7 years
Sd = 8.1 years		 European White British Subset UKB —