Polygenic Score (PGS) ID: PGS000790

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS Catalog: May 28, 2021
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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_IV
Development Method
Name 24 variants from Graff et al (PGS000079) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 24
Effect Weight Type Inverse-variance weighting
PGS Source
PGS Catalog Publication (PGP) ID PGP000186
Citation (link to publication) Kachuri L et al. Nat Commun (2020)
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 Cohort(s)
GWAS Catalog: GCST001267
Europe PMC: 21983787
 10,422 individuals European B58C, CNG, GenoMEL, UKBS
GWAS Catalog: GCST000437
Europe PMC: 19578364
 5,456 individuals European CNG, GenoMEL, WTCCC
GWAS Catalog: GCST001886
Europe PMC: 23455637
 4,919 individuals European GenoMEL, WTCCC
GWAS Catalog: GCST003061
Europe PMC: 26237428
 36,077 individuals European NR
GWAS Catalog: GCST001266
Europe PMC: 21983785
 6,555 individuals European AMFS, BATS, Q-MEGA, QIMR
GWAS Catalog: GCST002514
Europe PMC: 24980573
 6,122 individuals European HPFS, NHS
GWAS Catalog: GCST004142
Europe PMC: 28212542
 291,407 individuals European 23andMe
GWAS Catalog: GCST001245
Europe PMC: 21926416
 2,830 individuals European MDACCS
GWAS Catalog: GCST000198
Europe PMC: 18488026
 1,728 individuals European Q-MEGA

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
PPM002061 PSS001018|
European Ancestry|
392,803 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident melanoma HR: 1.44 [1.37, 1.5] AUROC: 0.654
C-index: 0.664 (0.008)		 R²: 0.18 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
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 —