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
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

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)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
36,077 individuals (100%)
Score Development/Training
European: 100%
3,666 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003061
Europe PMC: 26237428
36,077 individuals European NR
Score Development/Training
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
[
  • 1,892 cases
  • , 1,774 controls
]
,
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

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)
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

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