Polygenic Score (PGS) ID: PGS002253

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS Catalog: Feb. 16, 2022
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Score Details

Score Construction
PGS Name Melanoma_PRS45
Development Method
Name Previously published PGS (PMID:29890168) with update effect weights (by dosage)
Parameters genome-wide significant variants: p < 5 x 10-8 and one variant (MITF rs149617956) with robust association from whole-genome sequencing
Variants
Original Genome Build GRCh37
Number of Variants 45
Effect Weight Type log(OR) for the effect allele *NOTE* a EAF-normalised weight was used for the PRS (see "variant_description" and dosage_#_weight columns)
PGS Source
PGS Catalog Publication (PGP) ID PGP000274
Citation (link to publication) Steinberg J et al. Br J Dermatol (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
42,399 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 26237428
[
  • 15,990 cases
  • , 26,409 controls
]
 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
PPM012814 PSS009567|
European Ancestry|
4,765 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma HR: 1.25 [1.1, 1.42] — — age, sex, self-reported ethnicity, ease of tanning, 20 genetic PCs subdistribution hazard ratio (and 95% confidence interval) per 1 sd of PRS on log-scale, based on Fine-Grey competing risks regression with death as competing risk
PPM012817 PSS009568|
European Ancestry|
395,647 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma — AUROC: 0.662 [0.649, 0.675] R²: 0.051 [0.043, 0.06] age, sex AUC (and 95% confidence interval) for PRS-adjusted age-sex-specific absolute 10-year risk of invasive melanoma; R2 (and 95% confidence interval) based on 1.5% melanoma prevalence for same risk estimates as AUC (95% confidence interval)
PPM012820 PSS009567|
European Ancestry|
4,765 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma — AUROC: 0.653 [0.62, 0.686] R²: 0.046 [0.028, 0.068] age, sex AUC (and 95% confidence interval) for PRS-adjusted age-sex-specific absolute 10-year risk of invasive melanoma; R2 (and 95% confidence interval) based on 1.5% melanoma prevalence for same risk estimates as AUC (95% confidence interval)
PPM012811 PSS009568|
European Ancestry|
395,647 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma HR: 1.61 [1.53, 1.69] — — age, sex, self-reported ethnicity, ease of tanning, 20 genetic PCs subdistribution hazard ratio (and 95% confidence interval) per 1 sd of PRS on log-scale, based on Fine-Grey competing risks regression with death as competing risk

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
PSS009567 invasive melanoma diagnosis record (ICD10 code C43) in Victorian Cancer Registry or the Australian Cancer Database Mean = 9.7 years
[
  • 303 cases
  • , 4,462 controls
]
,
39.4 % Male samples
 Mean = 63.52 years
Sd = 7.21 years		 European — MCCS —
PSS009568 invasive melanoma diagnosis (ICD10 code C43 or ICD9 code 172 for ICD9) in cancer registry records (provided by NHS Digital for England and Wales, and National Records of Scotland, NHS Central Register for Scotland) Mean = 7.16 years
[
  • 1,651 cases
  • , 393,996 controls
]
,
46.4 % Male samples
 Mean = 56.91 years
Sd = 7.95 years		 European — UKB —