Polygenic Score (PGS) ID: PGS000079

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS Catalog: Feb. 12, 2020
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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
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 24
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
365,516 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

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

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. Nat Commun (2021)
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
PPM002045 PSS001018|
European Ancestry|
392,803 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.
Reported Trait: Incident melanoma HR: 1.43 [1.36, 1.49] AUROC: 0.652
C-index: 0.663 (0.008)
Age at assessment, sex, genotyping array, PCs(1-15), frequency of UV protection use (always vs. most times vs. never out in the sun vs. never), time outdoors in summer (hours per day), ease of tanning (very easily, vs. moderate vs mild vs. mostly burn) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS001018 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases.
[
  • 1,805 cases
  • , 390,998 controls
]
European UKB