PGS Publication: PGP000106

Publication Information (EuropePMC)
Title Multiplex melanoma families are enriched for polygenic risk.
PubMed ID 32716505(Europe PMC)
doi 10.1093/hmg/ddaa156
Publication Date Oct. 1, 2020
Journal Hum Mol Genet
Author(s) Law MH, Aoude LG, Duffy DL, Long GV, Johansson PA, Pritchard AL, Khosrotehrani K, Mann GJ, Montgomery GW, Iles MM, Cust AE, Palmer JM, Melanoma GWAS Consortium , Shannon KF, Spillane AJ, Stretch JR, Thompson JF, Saw RPM, Scolyer RA, Martin NG, Hayward NK, MacGregor S.
Released in PGS Catalog: Nov. 5, 2020

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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PGS Developed By This Publication

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)
PGS000339
(PRS22_CM)
 PGP000106 |
Law MH et al. Hum Mol Genet (2020)
 Cutaneous melanoma cutaneous melanoma 22
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000339/ScoringFiles/PGS000339.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) 		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
PPM000922 PGS000339
(PRS22_CM)
 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 PGS000339
(PRS22_CM)
 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

Evaluated Samples

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 —
[
  • 111 cases
  • , 1,774 controls
]
,
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 —
[
  • 1,292 cases
  • , 1,774 controls
]
,
46.28 % Male samples
 — European Australia BATS, QFMP —