| 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 |
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] | — | — |
|
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 | — | [
|
Mean = 59.0 years Sd = 16.0 years |
European | — | TCGA | — |
| PSS000277 | — | — | [
|
— | European | — | eMERGE | — |