Polygenic Score (PGS) ID: PGS000408

Predicted Trait
Reported Trait Melanomas of skin (diagnosis or history)
Mapped Trait(s) melanoma (EFO_0000756)
Additional Trait Information PheCode 172.1
Released in PGS Catalog: Dec. 15, 2020
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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 PRSWEB_PHECODE172.1_20001-1059_P_5e-08_MGI_20200608
Development Method
Name GWAS Hits
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
Variants
Original Genome Build GRCh37
Number of Variants 10
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
361,141 individuals (100%)
Score Development/Training
European: 100%
12,594 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
[
  • 2,898 cases
  • , 358,243 controls
]
EuropeanNR
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Score Development/Training
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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: 32991828
[
  • 1,376 cases
  • , 11,218 controls
]
EuropeanMGIPheCode:172.1; ICD9CM:172.0, 172.1, 172.2, 172.3, 172.4, 172.5, 172.6, 172.7, 172.8, 172.9, V10.82; ... ICD10CM:C43, C43.0, C43.1, C43.10, C43.11, C43.12, C43.2, C43.20, C43.21, C43.22, C43.3, C43.30, C43.31, C43.39, C43.4, C43.5, C43.51, C43.52, C43.59, C43.6, C43.60, C43.61, C43.62, C43.7, C43.70, C43.71, C43.72, C43.8, C43.9, D03, D03.0, D03.1, D03.10, D03.11, D03.12, D03.2, D03.20, D03.21, D03.22, D03.3, D03.30, D03.39, D03.4, D03.5, D03.51, D03.52, D03.59, D03.6, D03.60, D03.61, D03.62, D03.7, D03.70, D03.71, D03.72, D03.8, D03.9Show more————
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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.

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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
PPM001093PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hxOR: 1.384 [1.311, 1.461]
β: 0.325 (0.0276)		AUROC: 0.576 [0.561, 0.593]Nagelkerke's Pseudo-R²: 0.0217
Brier score: 0.0957
Odds Ratio (OR, top 1% vs. Rest): 2.25 [1.48, 3.42]		age, sex, batch PCs 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_20001-1059_P_5e-08_MGI_20200608
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Evaluated Samples

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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
PSS000543PheCode:172.1; ICD9CM:172.0, 172.1, 172.2, 172.3, 172.4, 172.5, 172.6, 172.7, 172.8, 172.9, V10.82; ... ICD10CM:C43, C43.0, C43.1, C43.10, C43.11, C43.12, C43.2, C43.20, C43.21, C43.22, C43.3, C43.30, C43.31, C43.39, C43.4, C43.5, C43.51, C43.52, C43.59, C43.6, C43.60, C43.61, C43.62, C43.7, C43.70, C43.71, C43.72, C43.8, C43.9, D03, D03.0, D03.1, D03.10, D03.11, D03.12, D03.2, D03.20, D03.21, D03.22, D03.3, D03.30, D03.39, D03.4, D03.5, D03.51, D03.52, D03.59, D03.6, D03.60, D03.61, D03.62, D03.7, D03.70, D03.71, D03.72, D03.8, D03.9Show more—
[
  • 1,325 cases
  • , 10,649 controls
]
—European—MGI—
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