| Predicted Trait | |
| Reported Trait | Melanoma |
| Mapped Trait(s) | melanoma (EFO_0000756) |
| Score Construction | |
| PGS Name | CC_Melanoma |
| Development Method | |
| Name | Genome-wide significant variants |
| Parameters | P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3 |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 24 |
| Effect Weight Type | log(OR) |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000050 |
| Citation (link to publication) | Graff RE et al. Nat Commun (2021) |
| Ancestry Distribution | |
| Source of Variant Associations (GWAS) | European: 100% 365,516 individuals (100%) |
| PGS Evaluation | European: 100% 3 Sample Sets |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST001267 Europe PMC: 21983787 |
10,422 individuals | European | NR |
GWAS Catalog: GCST000437 Europe PMC: 19578364 |
5,456 individuals | European | NR |
GWAS Catalog: GCST000198 Europe PMC: 18488026 |
1,728 individuals | European | Q-MEGA |
GWAS Catalog: GCST001886 Europe PMC: 23455637 |
4,919 individuals | European | NR |
GWAS Catalog: GCST003061 Europe PMC: 26237428 |
36,077 individuals | European | NR |
GWAS Catalog: GCST001266 Europe PMC: 21983785 |
6,555 individuals | European | AMFS, BATS, Q-MEGA, QIMR |
GWAS Catalog: GCST004142 Europe PMC: 28212542 |
291,407 individuals | European | 23andMe |
GWAS Catalog: GCST002514 Europe PMC: 24980573 |
6,122 individuals | European | HPFS, NHS |
GWAS Catalog: GCST001245 Europe PMC: 21926416 |
2,830 individuals | European | MDACCS |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PPM000199 | PSS000118| European Ancestry| 417,136 individuals |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Reported Trait: Melanoma | OR: 1.44 [1.41, 1.48] | — | — | Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. | Results from meta-analysis of GERA and UKB |
| PPM002045 | PSS001018| European Ancestry| 392,803 individuals |
PGP000186 | Kachuri L et al. Nat Commun (2020) |Ext. |
Reported Trait: Incident melanoma | HR: 1.43 [1.36, 1.49] | AUROC: 0.652 C-index: 0.663 (0.008) |
— | Age at assessment, sex, genotyping array, PCs(1-15), frequency of UV protection use (always vs. most times vs. never out in the sun vs. never), time outdoors in summer (hours per day), ease of tanning (very easily, vs. moderate vs mild vs. mostly burn) | C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years. |
| PPM017167 | PSS010153| European Ancestry| 1,200 individuals |
PGP000443 | Byrne S et al. Int J Epidemiol (2023) |Ext. |
Reported Trait: Melanoma | HR: 1.41 [1.33, 1.49] | — | — | age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS010153 | — | — | [
|
— | European | — | UKB | — |
| PSS000118 | Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 25010 | — | [ ,
46.0 % Male samples |
Mean = 58.0 years | European | — | GERA, UKB | — |
| PSS001018 | Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. | — | [
|
— | European | — | UKB | — |