| Predicted Trait | |
| Reported Trait | Cutaneous melanoma |
| Mapped Trait(s) | cutaneous melanoma (EFO_0000389) |
| Score Construction | |
| PGS Name | PRS22_CM |
| Development Method | |
| Name | Clumping and Thresholding (C+T) |
| Parameters | p <5e-6, LD reference panel = 5000 UK Biobank participants, LD r2 thresholds = 0.5 and 0.025 |
| Variants | |
| Original Genome Build | hg19 |
| Number of Variants | 22 |
| Effect Weight Type | log(OR) |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000106 |
| Citation (link to publication) | Law MH et al. Hum Mol Genet (2020) |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST003061 Europe PMC: 26237428 |
36,077 individuals | European | NR |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) | Phenotype Definitions & Methods | Age of Study Participants | Participant Follow-up Time | Additional Ancestry Description | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|---|
Europe PMC: 32716505 |
[ ,
53.16 % Male samples |
European | BATS, MIA, PAH | For MIA: Patients with histophatologically confirmed melanoma with germine DNA avaialbe from blood samples in th MIA Biospecimen Bank were included. For PAH: Patients whose locally invasive primary melanoma was confirmed by histopathology were recruited. For BATS: Individuals who self-reported as being free from melanoma and had no family history of melanoma were included. | — | — | Australia | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PPM000922 | PSS000464| European Ancestry| 1,885 individuals |
PGP000106 | Law MH et al. Hum Mol Genet (2020) |
Reported Trait: Cutaneous melanoma in multiplex melanoma families | — | — | Difference of PRS (deltaPRS; unaffected melanoma family members vs. unrelated controls): 0.347 (0.104) | PCs (1-10) | *Sample overlap between the controls used in this analysis and score development |
| PPM000921 | PSS000463| European Ancestry| 3,066 individuals |
PGP000106 | Law MH et al. Hum Mol Genet (2020) |
Reported Trait: Cutaneous melanoma in multiplex melanoma families | — | — | Difference of PRS (deltaPRS; melanoma family cases vs. unrelated controls): 0.505 (0.036) | PCs (1-10) | *Sample overlap between the controls used in this analysis and score development |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000464 | Unaffected family members from families with increased melaona risk. Recruited families were ranked as low-, medium- or high-risk using a risk index (T) that factored in the number of confirmed cases of melanoma versus number of unaffected family members, ages and year of birth | — | [ ,
46.37 % Male samples |
— | European | Australia | BATS, QFMP | — |
| PSS000463 | Unaffected family members from families with increased melaona risk. Recruited families were ranked as low-, medium- or high-risk using a risk index (T) that factored in the number of confirmed cases of melanoma versus number of unaffected family members, ages and year of birth | — | [ ,
46.28 % Male samples |
— | European | Australia | BATS, QFMP | — |