Polygenic Score (PGS) ID: PGS000766

Predicted Trait
Reported Trait Cutaneous melanoma
Mapped Trait(s) cutaneous melanoma (EFO_0000389)
Released in PGS Catalog: May 28, 2021
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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 PRS56_CM
Development Method
Name Variants associated with melanoma
Parameters GRCh38
Variants
Original Genome Build NR
Number of Variants 56
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000172
Citation (link to publication) Bakshi A et al. J Natl Cancer Inst (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
411,948 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: GCST010304
Europe PMC: 32341527
 411,948 individuals European 18 cohorts
  • 23andMe
  • ,AMFS
  • ,CPSII
  • ,DEMOKRITOS
  • ,Essen-Heidelberg
  • ,GenoMEL
  • ,HPFS
  • ,LMC
  • ,MDACCS
  • ,MELARISK
  • ,MIA
  • ,NHS
  • ,PAH
  • ,PLCO
  • ,Q-MEGA
  • ,SEARCH
  • ,UKB
  • ,WAMHS

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
PPM001963 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Incident cutaneous melanoma — — Hazard Ratio (HR, top 20% vs bottom 20%): 2.51 [1.28, 4.92] — Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001964 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Incident cutaneous melanoma (males) — — Hazard Ratio (HR, top 20% vs bottom 20%): 3.7 [1.37, 9.98] — Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001965 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Incident cutaneous melanoma (males) — — Hazard Ratio (HR, middle 60% vs bottom 20%): 2.61 [1.03, 6.63] — Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001966 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Prevalent cutaneous melanoma OR: 1.55 [1.42, 1.69] AUROC: 0.64 [0.62, 0.66] Odds Ratio (OR, top 20% vs bottom 20%): 3.66 [2.69, 5.05] Sex, family history Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001967 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Prevalent cutaneous melanoma (males) OR: 1.39 [1.23, 1.57] — — Family history Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001968 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Prevalent cutaneous melanoma (females) OR: 1.72 [1.53, 1.94] — — Family history Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001962 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Incident cutaneous melanoma HR: 1.46 [1.2, 1.77] C-index: 0.643 [0.584, 0.702] — Sex, melanoma family history, treatment (aspirin/placebo), age at enrolment, PRS*treatment Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.

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
PSS000982 Cases were individuals with cutaneous melanoma. Of the 628 cases, 528 were prevalent melanoma, whilst 98 were incident melanoma cases. Endpoints used were primary invasive cutaneous melanoma and metastatic melanoma with unknown primary location occurring during the trial (incident). Metastatic recurrence was excluded. Incident melanomas were confirmed by expert panel using histopathology, imaging of metastasis or other clinical evidence. If a participant had two events during the trial, the time of the first event was used. Prevalent melanomas occurring pre-trial were self-reported by participants but not confirmed by review of medical records and assumed to be invasive. Age at diagnosis for self-reported melanomas was reported as either before or after 50 years. Median = 4.7 years
[
  • 626 cases
  • , 12,086 controls
]
,
45.0 % Male samples
 Mean = 75.0 years
Sd = 4.23 years		 European — ASPREE —