Polygenic Score (PGS) ID: PGS004869

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
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_breast_cancer
Development Method
Name megaprs.auto
Parameters BayesR, p1=0.88, p2=0.1, p3=0.01, p4=0.01
Variants
Original Genome Build GRCh37
Number of Variants 872,060
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%
139,274 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004988
Europe PMC: 29059683
 139,274 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
PPM021136 PSS011557|
European Ancestry|
36,886 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Breast Cancer HR: 1.63 [1.55, 1.71] C-index: 0.63 [0.61, 0.64] — PCs 1-10 —
PPM021137 PSS011556|
European Ancestry|
17,370 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Breast Cancer HR: 1.48 [1.43, 1.54] C-index: 0.63 [0.62, 0.65] — PCs 1-10 —
PPM021138 PSS011554|
European Ancestry|
24,387 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Breast Cancer HR: 1.63 [1.42, 1.88] — — PCs 1-10 —
PPM021139 PSS011555|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Breast Cancer HR: 1.42 [1.3, 1.55] C-index: 0.61 [0.59, 0.64] — PCs 1-10 —
PPM021140 PSS011553|
European Ancestry|
230,276 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Breast Cancer HR: 1.61 [1.59, 1.64] C-index: 0.64 [0.63, 0.64] — PCs 1-10 —
PPM021141 PSS011552|
European Ancestry|
130,985 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Breast Cancer HR: 1.59 [1.53, 1.65] C-index: 0.63 [0.62, 0.64] — PCs 1-10 —
PPM021134 PSS011559|
European Ancestry|
242,571 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Breast Cancer HR: 1.67 [1.64, 1.7] — — PCs 1-10 —
PPM021135 PSS011558|
European Ancestry|
21,171 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Breast Cancer HR: 1.55 [1.49, 1.63] C-index: 0.62 [0.61, 0.63] — 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
PSS011552 — —
[
  • 2,610 cases
  • , 128,375 controls
]
 — European — EB —
PSS011553 — —
[
  • 18,037 cases
  • , 212,239 controls
]
 — European — FinnGen —
PSS011554 — —
[
  • 195 cases
  • , 24,192 controls
]
 — European — G&H —
PSS011555 — —
[
  • 510 cases
  • , 6,508 controls
]
 — European — GS:SFHS —
PSS011556 — —
[
  • 2,744 cases
  • , 14,626 controls
]
 — European — GEL —
PSS011557 — —
[
  • 1,596 cases
  • , 35,290 controls
]
 — European — HUNT —
PSS011558 — —
[
  • 2,114 cases
  • , 19,057 controls
]
 — European — MGBB —
PSS011559 — —
[
  • 15,232 cases
  • , 227,339 controls
]
 — European — UKB —