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(Variants and weights)

Polygenic Score (PGS) ID: PGS000079

Predicted Trait

Reported Trait: Melanoma
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): melanoma

Score Details

Name: CC_Melanoma

Original Genome Build: GRCh37
Number of Variants: 24

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001245
PubMed: 21926416
2,830 individuals European
GWAS Catalog: GCST001267
PubMed: 21983787
10,422 individuals European
GWAS Catalog: GCST000437
PubMed: 19578364
5,456 individuals European
GWAS Catalog: GCST000198
PubMed: 18488026
1,728 individuals European
GWAS Catalog: GCST001886
PubMed: 23455637
4,919 individuals European
GWAS Catalog: GCST003061
PubMed: 26237428
36,077 individuals European
GWAS Catalog: GCST001266
PubMed: 21983785
6,555 individuals European
GWAS Catalog: GCST004142
PubMed: 28212542
291,407 individuals European
GWAS Catalog: GCST002514
PubMed: 24980573
6,122 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000199 PSS000118 Graff RE et al. (2020) Reported Trait: Melanoma OR: 1.44 [1.41 - 1.48] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000118 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 25010 417,136 individuals
[ 6,782 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB