| Publication Information (EuropePMC) | |
| Title | Assessing the Incremental Contribution of Common Genomic Variants to Melanoma Risk Prediction in Two Population-Based Studies. |
| PubMed ID | 29890168(Europe PMC) |
| doi | 10.1016/j.jid.2018.05.023 |
| Publication Date | June 8, 2018 |
| Journal | J Invest Dermatol |
| Author(s) | Cust AE, Drummond M, Kanetsky PA, Australian Melanoma Family Study Investigators, Leeds Case-Control Study Investigators, Goldstein AM, Barrett JH, MacGregor S, Law MH, Iles MM, Bui M, Hopper JL, Brossard M, Demenais F, Taylor JC, Hoggart C, Brown KM, Landi MT, Newton-Bishop JA, Mann GJ, Bishop DT. |
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000744 (PRS_melanoma_pigment.pathway) |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Melanoma | melanoma | 31 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000744/ScoringFiles/PGS000744.txt.gz |
| PGS000743 (PRS_melanoma) |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Melanoma | melanoma | 45 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000743/ScoringFiles/PGS000743.txt.gz |
| PGS000745 (PRS_melanoma_telomere.pathway) |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Melanoma | melanoma | 9 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000745/ScoringFiles/PGS000745.txt.gz |
|
PGS Performance Metric ID (PPM) |
Evaluated Score |
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM001827 | PGS000743 (PRS_melanoma) |
PSS000928| European Ancestry| 1,460 individuals |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Reported Trait: Melanoma | OR: 1.63 [1.46, 1.83] | — | Odds Ratio (OR, top vs. bottom tertile): 2.84 [2.14, 3.77] Odds Ratio (OR, top vs. bottom decile): 5.62 [3.41, 9.29] |
Age, sex, self reported European ancestry | Overlap between testing and score development samples, testing <10% of score development |
| PPM001829 | PGS000743 (PRS_melanoma) |
PSS000928| European Ancestry| 1,460 individuals |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Reported Trait: Melanoma | — | AUROC: 0.68 [0.65, 0.71] | — | Traditional risk factors (hair colour, skin colour, eye colour, freckling as an adult, skin photosensitivity, self reported nevi, sunbed use, keratinocyte cancer personal history, first degree family history of melanoma, vacation sun exposure, blistering sunburns as a child), age, sex, self-reported European ancestry | — |
| PPM001830 | PGS000744 (PRS_melanoma_pigment.pathway) |
PSS000927| European Ancestry| 1,035 individuals |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Reported Trait: Melanoma | OR: 1.71 [1.49, 1.96] | — | Odds Ratio (OR, top vs. bottom tertile): 3.11 [2.21, 4.36] Odds Ratio (OR, top vs. bottom decile): 5.75 [3.09, 10.72] |
Age, sex, recruitment city, self-reported European ancestry | — |
| PPM001831 | PGS000744 (PRS_melanoma_pigment.pathway) |
PSS000928| European Ancestry| 1,460 individuals |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Reported Trait: Melanoma | OR: 1.66 [1.49, 1.86] | — | Odds Ratio (OR, top vs. bottom tertile): 2.94 [2.23, 3.88] Odds Ratio (OR, top vs. bottom decile): 7.0 [4.12, 11.88] |
Age, sex, self reported European ancestry | — |
| PPM001832 | PGS000745 (PRS_melanoma_telomere.pathway) |
PSS000927| European Ancestry| 1,035 individuals |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Reported Trait: Melanoma | OR: 1.15 [1.01, 1.31] | — | Odds Ratio (OR, top vs. bottom tertile): 1.4 [1.01, 1.93] | Age, sex, recruitment city, self-reported European ancestry | — |
| PPM001833 | PGS000745 (PRS_melanoma_telomere.pathway) |
PSS000928| European Ancestry| 1,460 individuals |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Reported Trait: Melanoma | OR: 1.18 [1.06, 1.31] | — | Odds Ratio (OR, top vs. bottom tertile): 1.55 [1.19, 2.02] Odds Ratio (OR, top vs. bottom decile): 2.0 [1.24, 3.23] |
Age, sex, self reported European ancestry | — |
| PPM001826 | PGS000743 (PRS_melanoma) |
PSS000927| European Ancestry| 1,035 individuals |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Reported Trait: Melanoma | OR: 1.75 [1.53, 2.01] | — | Odds Ratio (OR, top vs. bottom tertile): 3.22 [2.3, 4.51] Odds Ratio (OR, top vs. bottom decile): 5.88 [3.14, 11.03] |
Age, sex, recruitment city, self-reported European ancestry | Overlap between testing and score development samples, testing <10% of score development |
| PPM001828 | PGS000743 (PRS_melanoma) |
PSS000927| European Ancestry| 1,035 individuals |
PGP000151 | Cust AE et al. J Invest Dermatol (2018) |
Reported Trait: Melanoma | — | AUROC: 0.74 [0.71, 0.77] | — | Traditional risk factors (hair colour, skin colour, eye colour, freckling as an adult, skin photosensitivity, self reported nevi, sunbed use, keratinocyte cancer personal history, first degree family history of melanoma, vacation sun exposure, blistering sunburns as a child), age, sex, recruitment city, self-reported European ancestry | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000927 | Cases include invasive cutaneous melanoma diagnoses between ages 18 and 39 years | — | [ ,
40.0 % Male samples |
— | European | — | AMFS | — |
| PSS000928 | Cases include histopathologically confirmed invasive melanoma cases in patients between 18 and 82 years. | — | [ ,
40.0 % Male samples |
— | European | — | LMC | — |