Polygenic Score (PGS) ID: PGS000430

Predicted Trait
Reported Trait Melanomas of skin (diagnosis or history)
Mapped Trait(s) melanoma (EFO_0000756)
Additional Trait Information PheCode 172.1
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608
Development Method
Name PRS-CS
Parameters Parameters = auto; LD reference (eur)
Variants
Original Genome Build GRCh37
Number of Variants 1,119,238
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
397,762 individuals (100%)
Score Development/Training
European: 100%
12,594 individuals (100%)
PGS Evaluation
European: 100%
10 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 32424355
[
  • 2,691 cases
  • , 395,071 controls
]
 European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 32991828
[
  • 1,376 cases
  • , 11,218 controls
]
 European MGI PheCode:172.1; ICD9CM:172.0, 172.1, 172.2, 172.3, 172.4, 172.5, 172.6, 172.7, 172.8, 172.9, V10.82; ICD10CM:C43, C43.0, C43.1, C43.10, C43.11, C43.12, C43.2, C43.20, C43.21, C43.22, C43.3, C43.30, C43.31, C43.39, C43.4, C43.5, C43.51, C43.52, C43.59, C43.6, C43.60, C43.61, C43.62, C43.7, C43.70, C43.71, C43.72, C43.8, C43.9, D03, D03.0, D03.1, D03.10, D03.11, D03.12, D03.2, D03.20, D03.21, D03.22, D03.3, D03.30, D03.39, D03.4, D03.5, D03.51, D03.52, D03.59, D03.6, D03.60, D03.61, D03.62, D03.7, D03.70, D03.71, D03.72, D03.8, D03.9 — — — —

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
PPM001115 PSS000543|
European Ancestry|
11,974 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Melanomas of skin, dx or hx OR: 1.219 [1.151, 1.292]
β: 0.198 (0.0296)		 AUROC: 0.555 [0.54, 0.573] Nagelkerke's Pseudo-R²: 0.00721
Brier score: 0.0965
Odds Ratio (OR, top 1% vs. Rest): 1.64 [1.01, 2.66]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608
PPM018439 PSS010977|
European Ancestry|
4,987 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Skin colour β: -0.02584 — R²: 0.01389 — —
PPM018440 PSS010970|
European Ancestry|
4,984 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Freckles β: 0.07956 — R²: 0.02392 — —
PPM018441 PSS010971|
European Ancestry|
4,985 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Ease suntan β: -0.0466 — R²: 0.01554 — —
PPM018442 PSS010976|
European Ancestry|
4,973 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Ease sunburn β: 0.05703 — R²: 0.012 — —
PPM018444 PSS010972|
European Ancestry|
4,933 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Phototype score β: -0.9044 — R²: 0.03608 — —
PPM018445 PSS010975|
European Ancestry|
4,985 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Fitzpatrick scale β: -0.04982 — R²: 0.03301 — —
PPM018446 PSS010978|
European Ancestry|
4,918 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Red hair β: 1.49896 — pseudo R²: 0.0406 — —
PPM018447 PSS010979|
European Ancestry|
4,352 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Brown hair β: 1.13169 — pseudo R²: 0.0684 — —
PPM018443 PSS010973|
European Ancestry|
4,933 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Sunscreen in exterior β: 0.03277 — R²: 0.03826 — —

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
PSS010971 — — 4,985 individuals — European — NR GCAT
PSS010972 — — 4,933 individuals — European — NR GCAT
PSS010973 — — 4,933 individuals — European — NR GCAT
PSS010975 — — 4,985 individuals — European — NR GCAT
PSS010976 — — 4,973 individuals — European — NR GCAT
PSS010977 — — 4,987 individuals — European — NR GCAT
PSS010978 — — 4,918 individuals — European — NR GCAT
PSS010979 — — 4,352 individuals — European — NR GCAT
PSS000543 PheCode:172.1; ICD9CM:172.0, 172.1, 172.2, 172.3, 172.4, 172.5, 172.6, 172.7, 172.8, 172.9, V10.82; ICD10CM:C43, C43.0, C43.1, C43.10, C43.11, C43.12, C43.2, C43.20, C43.21, C43.22, C43.3, C43.30, C43.31, C43.39, C43.4, C43.5, C43.51, C43.52, C43.59, C43.6, C43.60, C43.61, C43.62, C43.7, C43.70, C43.71, C43.72, C43.8, C43.9, D03, D03.0, D03.1, D03.10, D03.11, D03.12, D03.2, D03.20, D03.21, D03.22, D03.3, D03.30, D03.39, D03.4, D03.5, D03.51, D03.52, D03.59, D03.6, D03.60, D03.61, D03.62, D03.7, D03.70, D03.71, D03.72, D03.8, D03.9 —
[
  • 1,325 cases
  • , 10,649 controls
]
 — European — MGI —
PSS010970 — — 4,984 individuals — European — NR GCAT