Predicted Trait | |
Reported Trait | Melanoma |
Mapped Trait(s) | melanoma (EFO_0000756) |
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) |
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 |
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 |
---|---|---|---|---|---|---|---|---|
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] | — | — |
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 |
— | — |
PGS Sample Set ID (PSS ID) |
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 |
---|---|---|---|---|---|---|---|---|
PSS000277 | Primary tumor samples from TCGA | — | [
|
Mean = 59.0 years Sd = 16.0 years |
European | — | TCGA | — |
PSS000277 | — | — | [
|
— | European | — | eMERGE | — |