PGS Publication: PGP000478

Publication Information (EuropePMC)
Title Development and validation of genome-wide polygenic risk scores for predicting breast cancer incidence in Japanese females: a population-based case-cohort study.
PubMed ID 36538246(Europe PMC)
doi 10.1007/s10549-022-06843-6
Publication Date Dec. 20, 2022
Journal Breast Cancer Res Treat
Author(s) Ohbe H, Hachiya T, Yamaji T, Nakano S, Miyamoto Y, Sutoh Y, Otsuka-Yamasaki Y, Shimizu A, Yasunaga H, Sawada N, Inoue M, Tsugane S, Iwasaki M, Japan Public Health Center-based Prospective Study Group.
Released in PGS Catalog: July 5, 2023

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003758
(BrCa_PRS_JPHC_JPGWAS)
 PGP000478 |
Ohbe H et al. Breast Cancer Res Treat (2022)
 Breast cancer breast carcinoma 46,861
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003758/ScoringFiles/PGS003758.txt.gz
PGS003759
(BrCa_PRS_JPHC_EURGWAS)
 PGP000478 |
Ohbe H et al. Breast Cancer Res Treat (2022)
 Breast cancer breast carcinoma 17,252
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003759/ScoringFiles/PGS003759.txt.gz

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000004
(PRS313_BC)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Breast cancer breast carcinoma 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.txt.gz

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) 		Evaluated Score 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 PGS003758
(BrCa_PRS_JPHC_JPGWAS)
 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 —
PPM018545 PGS003759
(BrCa_PRS_JPHC_EURGWAS)
 PSS011015|
East Asian Ancestry|
8,001 individuals
 PGP000478 |
Ohbe H et al. Breast Cancer Res Treat (2022)
 Reported Trait: Incident breast cancer — C-index: 0.586 (0.018) Improvement in C-index from age-only model: 0.046
Hazard ratio (HR, high vs low tertile): 2.25 [1.51, 3.33]		 age —
PPM018546 PGS000004
(PRS313_BC)
 PSS011015|
East Asian Ancestry|
8,001 individuals
 PGP000478 |
Ohbe H et al. Breast Cancer Res Treat (2022)
|Ext.		 Reported Trait: Incident breast cancer — C-index: 0.582 (0.018) Improvement in C-index from age-only model: 0.042
Hazard ratio (HR, high vs low tertile): 1.89 [1.25, 2.86]		 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 —