Polygenic Score (PGS) ID: PGS000118

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

Score Details

Score Construction
PGS Name MEL29
Variants
Original Genome Build GRCh37
Number of Variants 29
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.
PGS Source
PGS Catalog Publication (PGP) ID PGP000055
Citation (link to publication) Fritsche LG et al. PLoS Genet (2019)

Contributing Samples

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

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000339 PSS000206 PGP000055
Fritsche LG et al. (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 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Skin cancer OR: 1.3[1.26, 1.34] AUROC: 0.57[0.56, 0.58] age, sex, batch, PC1-4
PPM000345 PSS000211 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Skin cancer OR: 1.2[1.22, 1.36] age, sex, genotyping array, first 4 genotype PCs
PPM000348 PSS000210 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Melanoma OR: 1.5[1.44, 1.55] age, sex, genotyping array, first 4 genotype PCs

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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