Polygenic Score (PGS) ID: PGS000332

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS: Sept. 18, 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 PRS_BC
Variants
Original Genome Build hg19
Number of Variants 6,390,808
Development Method
Name LDpred
Parameters ρ = 0.03; LD radius = 4000; LD reference panel = 2,690 Finnish individuals [autosomal variants only]
PGS Source
PGS Catalog Publication (PGP) ID PGP000100
Citation (link to publication) Mars N et al. Nat Med (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004988
EuropePMC: 29059683
139,274 individuals European
Score Development/Training
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
National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. 21,813 individuals,
47.3 % Male samples
Mean (Age At Baseline) = 48.0 years European
(Finnish)
FINRISK Used to select optimal threshold of ρ for all subsequent analyses. FINRISK surveys from 1992, 1997, 2002 and 2007

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000889 PSS000443 PGP000100
Mars N et al. (2020)
Reported Trait: Breast cancer (incident and prevalent cases) HR: 1.64[1.6, 1.69] genotyping array/batch, 10 ancestry PCs
PPM000899 PSS000444 PGP000100
Mars N et al. (2020)
Reported Trait: Incident breast cancer C-index: 0.75 age, family history of breast cancer, current smoking, BMI, alcohol use disorder, years of hormone replacement therapy, having given birth to one or more children, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000894 PSS000444 PGP000100
Mars N et al. (2020)
Reported Trait: Incident breast cancer C-index: 0.737 age, genotyping array/batch, 10 ancestry PCs 10-year risk

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000443 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 4,960 cases
  • , 71,213 controls
]
,
0.0 % Male samples
European
(Finnish)
FinnGen
PSS000444 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 742 cases
  • , 37,099 controls
]
European
(Finnish)
FinnGen