Polygenic Score (PGS) ID: PGS000335

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name BC_PRSCS
Development Method
Name PRS-CS
Parameters PRS-CS-auto, 1000G European sample (N = 503) as the external LD reference panel
Variants
Original Genome Build GRCh38
Number of Variants 1,079,089
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000102
Citation (link to publication) Mars N et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
PGS Evaluation
European: 100%
1 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

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
PPM000903 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
 Reported Trait: Breast cancer OR: 1.8 [1.76, 1.84] — — Age, 10 ancestry PCs, batch —
PPM000902 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
 Reported Trait: Breast cancer HR: 1.71 [1.68, 1.75] — — 10 ancestry PCs, batch, age as time scale —

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 —