Polygenic Score (PGS) ID: PGS000157

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS: April 29, 2020

Score Details

Score Construction
PGS Name cGRS_Melanoma
Variants
Original Genome Build NR
Number of Variants 17
Development Method
Name Pruning + Thresholding
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004142
EuropePMC: 28212542
291,407 individuals European
GWAS Catalog: GCST001267
EuropePMC: 21983787
10,422 individuals European
GWAS Catalog: GCST000438
EuropePMC: 19578365
1,524 individuals European
GWAS Catalog: GCST000437
EuropePMC: 19578364
5,456 individuals European
GWAS Catalog: GCST001124
EuropePMC: 21700618
8,058 individuals European
GWAS Catalog: GCST000198
EuropePMC: 18488026
1,728 individuals European

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000477 PSS000277 PGP000075
Shi Z et al. (2019)
Reported Trait: Melanoma Mean realative risk: 1.2[1.14, 1.26]
Wilcoxon test (case vs. control) p-value: 5.99e-11
PPM000488 PSS000277 PGP000075
Shi Z et al. (2019)
Reported Trait: Melanoma Odds Ratio (OR; high vs. average risk groups): 1.72[1.37, 2.16]

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000277 Primary tumor samples from TCGA
[
  • 450 cases
  • , 0 controls
]
Mean = 59.0 years
Sd = 16.0 years
European TCGA
PSS000277
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE