Polygenic Score (PGS) ID: PGS000423

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
Download Score FTP directory
Terms and Licenses
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 PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_PT_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 29
Development Method
Name P&T
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=1e-06
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%
356,564 individuals (100%)
Score Development/Training
European: 100%
12,594 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST000437
Europe PMC: 19578364
5,456 individuals European
GWAS Catalog: GCST001266
Europe PMC: 21983785
6,555 individuals European
GWAS Catalog: GCST001267
Europe PMC: 21983787
10,422 individuals European
GWAS Catalog: GCST001886
Europe PMC: 23455637
4,919 individuals European
GWAS Catalog: GCST003061
Europe PMC: 26237428
36,077 individuals European
GWAS Catalog: GCST004142
Europe PMC: 28212542
291,407 individuals European
GWAS Catalog: GCST000198
Europe PMC: 18488026
1,728 individuals European
Score Development/Training
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
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
[
  • 1,376 cases
  • , 11,218 controls
]
European MGI

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
PPM001108 PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx β: 0.394 (0.0301)
OR: 1.484 [1.399, 1.574]
AUROC: 0.608 [0.592, 0.623] Nagelkerke's Pseudo-R²: 0.0289
Brier score: 0.0954
Odds Ratio (OR, top 1% vs. Rest): 2.93 [2.0, 4.3]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_PT_MGI_20200608

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
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