Polygenic Score (PGS) ID: PGS004875

Predicted Trait
Reported Trait All Cancers
Mapped Trait(s) cancer (MONDO_0004992)
Released in PGS Catalog: June 27, 2024
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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 INTERVENE_MegaPRS_AllCancers
Development Method
Name megaprs.auto
Parameters bolt, p=0.02, f2=0.35
Variants
Original Genome Build GRCh37
Number of Variants 818,872
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
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
7 Sample Sets

Development Samples

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
PPM021181 PSS011657|
European Ancestry|
38,448 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Cancer HR: 0.9 [0.89, 0.91] C-index: 0.53 [0.53, 0.54] — PCs 1-10 —
PPM021182 PSS011656|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Cancer HR: 1.13 [1.11, 1.15] C-index: 0.54 [0.53, 0.54] — PCs 1-10 —
PPM021183 PSS011655|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Cancer HR: 1.06 [1.04, 1.08] C-index: 0.54 [0.53, 0.55] — PCs 1-10 —
PPM021184 PSS011653|
European Ancestry|
44,177 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Cancer HR: 1.15 [1.08, 1.23] — — PCs 1-10 —
PPM021185 PSS011654|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Cancer HR: 1.1 [1.05, 1.14] C-index: 0.55 [0.53, 0.56] — PCs 1-10 —
PPM021187 PSS011651|
European Ancestry|
199,868 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Cancer HR: 1.15 [1.13, 1.16] C-index: 0.54 [0.53, 0.55] — PCs 1-10 —
PPM021186 PSS011652|
European Ancestry|
412,090 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Cancer HR: 1.17 [1.16, 1.17] C-index: 0.54 [0.54, 0.55] — 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
PSS011651 — —
[
  • 16,701 cases
  • , 183,167 controls
]
 — European — EB —
PSS011652 — —
[
  • 72,760 cases
  • , 339,330 controls
]
 — European — FinnGen —
PSS011653 — —
[
  • 912 cases
  • , 43,265 controls
]
 — European — G&H —
PSS011654 — —
[
  • 2,002 cases
  • , 5,016 controls
]
 — European — GS:SFHS —
PSS011655 — —
[
  • 12,187 cases
  • , 17,240 controls
]
 — European — GEL —
PSS011656 — —
[
  • 10,696 cases
  • , 59,019 controls
]
 — European — HUNT —
PSS011657 — —
[
  • 15,217 cases
  • , 23,231 controls
]
 — European — MGBB —