Polygenic Score (PGS) ID: PGS004886

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS Catalog: June 27, 2024
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 INTERVENE_MegaPRS_Melanoma
Development Method
Name megaprs.auto
Parameters lasso-shrink
Variants
Original Genome Build GRCh37
Number of Variants 692,834
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000618
Citation (link to publication) Jermy B et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
417,127 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90011809
Europe PMC: 32887889
 417,127 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
— 404 individuals European 1000G — — — non-Finnish Europeans —

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
PPM021259 PSS011668|
European Ancestry|
38,448 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Melanoma HR: 1.18 [1.15, 1.21] C-index: 0.58 [0.57, 0.59] — PCs 1-10 —
PPM021261 PSS011618|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Melanoma HR: 1.35 [1.23, 1.49] C-index: 0.58 [0.54, 0.61] — PCs 1-10 —
PPM021262 PSS011617|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Melanoma HR: 1.43 [1.14, 1.79] C-index: 0.65 [0.59, 0.72] — PCs 1-10 —
PPM021263 PSS011616|
European Ancestry|
412,090 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Melanoma HR: 1.37 [1.32, 1.42] C-index: 0.59 [0.58, 0.61] — PCs 1-10 —
PPM021264 PSS011615|
European Ancestry|
199,868 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Melanoma HR: 1.18 [1.12, 1.24] C-index: 0.55 [0.54, 0.57] — PCs 1-10 —
PPM021260 PSS011619|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Melanoma HR: 1.32 [1.23, 1.4] C-index: 0.58 [0.56, 0.6] — PCs 1-10 —

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
PSS011615 — —
[
  • 1,329 cases
  • , 198,539 controls
]
 — European — EB —
PSS011616 — —
[
  • 2,969 cases
  • , 409,121 controls
]
 — European — FinnGen —
PSS011617 — —
[
  • 78 cases
  • , 6,940 controls
]
 — European — GS:SFHS —
PSS011618 — —
[
  • 400 cases
  • , 29,027 controls
]
 — European — GEL —
PSS011619 — —
[
  • 929 cases
  • , 68,786 controls
]
 — European — HUNT —
PSS011668 — —
[
  • 5,768 cases
  • , 32,680 controls
]
 — European — MGBB —