Polygenic Score (PGS) ID: PGS003758

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: July 5, 2023
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Score Details

Score Construction
PGS Name BrCa_PRS_JPHC_JPGWAS
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2 <= 0.2, p<=0.05
Variants
Original Genome Build GRCh37
Number of Variants 46,861
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000478
Citation (link to publication) Ohbe H et al. Breast Cancer Res Treat (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
95,283 individuals (100%)
Score Development/Training
East Asian: 100%
2,254 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90013695
Europe PMC: 32514122
 95,283 individuals East Asian
(Japanese)		 BBJ
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
—
[
  • 63 cases
  • , 2,191 controls
]
,
0.0 % Male samples
 East Asian
(Japanese)		 JPHC — Mean = 57.5 years
Sd = 7.3 years		 Median = 11.9 years — —

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
PPM018544 PSS011015|
East Asian Ancestry|
8,001 individuals
 PGP000478 |
Ohbe H et al. Breast Cancer Res Treat (2022)
 Reported Trait: Incident breast cancer — C-index: 0.598 (0.018) Improvement in C-index from age-only model: 0.058
Hazard ratio (HR, high vs low tertile): 2.47 [1.64, 3.7]		 age —

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
PSS011015 — Median = 16.9 years
[
  • 260 cases
  • , 7,741 controls
]
,
0.0 % Male samples
 Mean = 53.8 years
Sd = 7.8 years		 East Asian
(Japanese)		 — JPHC —