Polygenic Score (PGS) ID: PGS000332

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Sept. 18, 2020
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Score Details

Score Construction
PGS Name PRS_BC
Development Method
Name LDpred
Parameters ρ = 0.03; LD radius = 4000; LD reference panel = 2,690 Finnish individuals [autosomal variants only]
Variants
Original Genome Build hg19
Number of Variants 6,390,808
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000100
Citation (link to publication) Mars N et al. Nat Med (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
Score Development/Training
European: 100%
21,813 individuals (100%)
PGS Evaluation
European: 100%
3 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
— 21,813 individuals,
47.3 % Male samples
 European
(Finnish)		 FINRISK 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. Mean (Age At Baseline) = 48.0 years — — 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) 		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
PPM000899 PSS000444|
European Ancestry|
37,841 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
37,841 individuals
 PGP000100 |
Mars N et al. Nat Med (2020)
 Reported Trait: Incident breast cancer — C-index: 0.737 — age, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM001346 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
|Ext.		 Reported Trait: Breast cancer HR: 1.63 [1.6, 1.67] — — 10 ancestry PCs, batch, age as time scale —
PPM001348 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
|Ext.		 Reported Trait: Breast cancer OR: 1.71 [1.67, 1.75] — — Age, 10 ancestry PCs, batch —
PPM000889 PSS000443|
European Ancestry|
76,173 individuals
 PGP000100 |
Mars N et al. Nat Med (2020)
 Reported Trait: Breast cancer (incident and prevalent cases) HR: 1.64 [1.6, 1.69] — — genotyping array/batch, 10 ancestry PCs —

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
PSS000450 Breast cancer cases were identified through the Finnish Cancer Registry with diagnosis C50 (International Classification of Diseases for Oncology, 3rd Edition; ICD-O-3), from the drug reimbursement registry by selecting individuals with a reimbursement code for breast cancer, and from the death registry with ICD-10 C50. —
[
  • 8,401 cases
  • , 114,577 controls
]
,
0.0 % Male samples
 Mean Age (At The End Of Follow-Up) = 58.5 years
IQR = [45.1, 72.2] years		 European
(Finnish)		 — FinnGen —
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 —