PGS Publication: PGP000151

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.
Released in PGS Catalog: March 22, 2021

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000744 PRS_melanoma_pigment.pathway PGP000151
Cust AE et al. J Invest Dermatol (2018)
Melanoma melanoma 31 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000744/ScoringFiles/PGS000744.txt.gz
PGS000745 PRS_melanoma_telomere.pathway PGP000151
Cust AE et al. J Invest Dermatol (2018)
Melanoma melanoma 9 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000745/ScoringFiles/PGS000745.txt.gz
PGS000743 PRS_melanoma PGP000151
Cust AE et al. J Invest Dermatol (2018)
Melanoma melanoma 45 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000743/ScoringFiles/PGS000743.txt.gz

Performance Metrics

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)
Evaluated Score 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
PPM001827 PGS000743
(PRS_melanoma)
PSS000928 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 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 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 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 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 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 decile): 2.0 [1.24, 3.23]
Odds Ratio (OR, top vs. bottom tertile): 1.55 [1.19, 2.02]
Age, sex, self reported European ancestry
PPM001826 PGS000743
(PRS_melanoma)
PSS000927 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 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

Evaluated Samples

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
PSS000927 Cases include invasive cutaneous melanoma diagnoses between ages 18 and 39 years
[
  • 578 cases
  • , 457 controls
]
,
40.0 % Male samples
European AMFS
PSS000928 Cases include histopathologically confirmed invasive melanoma cases in patients between 18 and 82 years.
[
  • 964 cases
  • , 496 controls
]
,
40.0 % Male samples
European LMC