Polygenic Score (PGS) ID: PGS000079

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS Catalog: Feb. 12, 2020
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name CC_Melanoma
Variants
Original Genome Build GRCh37
Number of Variants 24
Development Method
Name Genome-wide significant SNPs
Parameters P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. bioRxiv (2020) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
365,516 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001267
Europe PMC: 21983787
10,422 individuals European
GWAS Catalog: GCST000437
Europe PMC: 19578364
5,456 individuals European
GWAS Catalog: GCST000198
Europe PMC: 18488026
1,728 individuals European
GWAS Catalog: GCST001886
Europe PMC: 23455637
4,919 individuals European
GWAS Catalog: GCST003061
Europe PMC: 26237428
36,077 individuals European
GWAS Catalog: GCST001266
Europe PMC: 21983785
6,555 individuals European
GWAS Catalog: GCST004142
Europe PMC: 28212542
291,407 individuals European
GWAS Catalog: GCST002514
Europe PMC: 24980573
6,122 individuals European
GWAS Catalog: GCST001245
Europe PMC: 21926416
2,830 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 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
PPM000199 PSS000118|
European Ancestry|
417,136 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
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 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
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
[
  • 6,782 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB