PGS Publication: PGP000172

Publication Information (EuropePMC)
Title Genomic Risk Score for Melanoma in a Prospective Study of Older Individuals.
PubMed ID 33837773(Europe PMC)
doi 10.1093/jnci/djab076
Publication Date April 10, 2021
Journal J Natl Cancer Inst
Author(s) Bakshi A, Yan M, Riaz M, Polekhina G, Orchard SG, Tiller J, Wolfe R, Joshi A, Cao Y, McInerney-Leo AM, Yanes T, Janda M, Soyer HP, Cust AE, Law MH, Gibbs P, McLean C, Chan AT, McNeil JJ, Mar VJ, Lacaze P.
Released in PGS Catalog: May 28, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000766
(PRS56_CM)
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Cutaneous melanoma cutaneous melanoma 56
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000766/ScoringFiles/PGS000766.txt.gz

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) 		Evaluated Score 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 PGS000766
(PRS56_CM)
 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 PGS000766
(PRS56_CM)
 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 PGS000766
(PRS56_CM)
 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 PGS000766
(PRS56_CM)
 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 PGS000766
(PRS56_CM)
 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 PGS000766
(PRS56_CM)
 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 PGS000766
(PRS56_CM)
 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 —