PGS Publication: PGP000274

Publication Information (EuropePMC)
Title Independent evaluation of melanoma polygenic risk scores in UK and Australian prospective cohorts.
PubMed ID 34921685(Europe PMC)
doi 10.1111/bjd.20956
Publication Date Dec. 18, 2021
Journal Br J Dermatol
Author(s) Steinberg J, Iles MM, Lee JY, Wang X, Law MH, Smit AK, Nguyen-Dumont T, Giles GG, Southey MC, Milne RL, Mann GJ, Bishop DT, MacInnis RJ, Cust AE.
Released in PGS Catalog: Feb. 16, 2022

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
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)
PGS002246
(Melanoma_PRS50)
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Melanoma melanoma 50
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002246/ScoringFiles/PGS002246.txt.gz
PGS002247
(Melanoma_PRS68)
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Melanoma melanoma 68
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002247/ScoringFiles/PGS002247.txt.gz
PGS002253
(Melanoma_PRS45)
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Melanoma melanoma 45
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002253/ScoringFiles/PGS002253.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
PPM012812 PGS002247
(Melanoma_PRS68)
 PSS009568|
European Ancestry|
395,647 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma HR: 1.8 [1.71, 1.88] — — 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
PPM012813 PGS002246
(Melanoma_PRS50)
 PSS009568|
European Ancestry|
395,647 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma HR: 1.73 [1.65, 1.81] — — 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
PPM012814 PGS002253
(Melanoma_PRS45)
 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
PPM012815 PGS002247
(Melanoma_PRS68)
 PSS009567|
European Ancestry|
4,765 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma HR: 1.47 [1.31, 1.67] — — 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
PPM012816 PGS002246
(Melanoma_PRS50)
 PSS009567|
European Ancestry|
4,765 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma HR: 1.47 [1.3, 1.66] — — 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 PGS002253
(Melanoma_PRS45)
 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)
PPM012818 PGS002247
(Melanoma_PRS68)
 PSS009568|
European Ancestry|
395,647 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma — AUROC: 0.685 [0.673, 0.698] R²: 0.068 [0.059, 0.078] 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)
PPM012819 PGS002246
(Melanoma_PRS50)
 PSS009568|
European Ancestry|
395,647 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma — AUROC: 0.678 [0.665, 0.691] R²: 0.062 [0.053, 0.072] 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 PGS002253
(Melanoma_PRS45)
 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)
PPM012821 PGS002247
(Melanoma_PRS68)
 PSS009567|
European Ancestry|
4,765 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma — AUROC: 0.691 [0.661, 0.722] R²: 0.072 [0.051, 0.1] 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)
PPM012822 PGS002246
(Melanoma_PRS50)
 PSS009567|
European Ancestry|
4,765 individuals
 PGP000274 |
Steinberg J et al. Br J Dermatol (2021)
 Reported Trait: Incident invasive melanoma — AUROC: 0.688 [0.657, 0.718] R²: 0.07 [0.048, 0.096] 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 PGS002253
(Melanoma_PRS45)
 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 —