Polygenic Score (PGS) ID: PGS000339

Predicted Trait
Reported Trait Cutaneous melanoma
Mapped Trait(s) cutaneous melanoma (EFO_0000389)
Released in PGS Catalog: Nov. 5, 2020
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Score Details

Score Construction
PGS Name PRS22_CM
Variants
Original Genome Build hg19
Number of Variants 22
Development Method
Name Clumping + Thresholding
Parameters p <5e-6, LD reference panel = 5000 UK Biobank participants, LD r2 thresholds = 0.5 and 0.025
PGS Source
PGS Catalog Publication (PGP) ID PGP000106
Citation (link to publication) Law MH et al. Hum Mol Genet (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003061
EuropePMC: 26237428
36,077 individuals European
Score Development/Training
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
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.
[
  • 1,892 cases
  • , 1,774 controls
]
,
53.16 % Male samples
European Australia BATS, MIA, PAH

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)
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
PPM000922 PSS000464 PGP000106
Law MH et al. (2020)
Reported Trait: Cutaneous melanoma in multiplex melanoma families Difference of PRS (deltaPRS; unaffected melanoma family members vs. unrelated controls): 0.347 PCs (1-10) *Sample overlap between the controls used in this analysis and score development
PPM000921 PSS000463 PGP000106
Law MH et al. (2020)
Reported Trait: Cutaneous melanoma in multiplex melanoma families Difference of PRS (deltaPRS; melanoma family cases vs. unrelated controls): 0.505 PCs (1-10) *Sample overlap between the controls used in this analysis and score development

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
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