Polygenic Score (PGS) ID: PGS000487

Predicted Trait
Reported Trait Breast cancer (female)
Mapped Trait(s) breast carcinoma (EFO_0000305)
Additional Trait Information PheCode 174.1
Released in PGS Catalog: Dec. 15, 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 PRSWEB_PHECODE174.1_GWAS-Catalog-r2019-05-03-X174.1_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=3.16e-09
Variants
Original Genome Build GRCh37
Number of Variants 62
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
559,287 individuals (100%)
Score Development/Training
European: 100%
7,368 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: GCST000036
Europe PMC: 17529973
 2,287 individuals European NR
GWAS Catalog: GCST000037
Europe PMC: 17529974
 13,145 individuals European NR
GWAS Catalog: GCST000162
Europe PMC: 18326623
 548 individuals European NR
GWAS Catalog: GCST000365
Europe PMC: 19330030
 2,287 individuals European NR
GWAS Catalog: GCST000678
Europe PMC: 20453838
 8,556 individuals European NR
GWAS Catalog: GCST000801
Europe PMC: 20852631
 2,383 individuals European NR
GWAS Catalog: GCST000811
Europe PMC: 20872241
 8,428 individuals European NR
GWAS Catalog: GCST000952
Europe PMC: 21263130
 6,346 individuals European NR
GWAS Catalog: GCST001012
Europe PMC: 21424380
 623 individuals European NR
GWAS Catalog: GCST001831
Europe PMC: 23354978
 1,001 individuals European NR
GWAS Catalog: GCST001916
Europe PMC: 23544013
 2,727 individuals European NR
GWAS Catalog: GCST001930
Europe PMC: 23535733
 39,387 individuals European NR
GWAS Catalog: GCST001937
Europe PMC: 23535729
 22,627 individuals European NR
GWAS Catalog: GCST004949
Europe PMC: 19330027
 754 individuals European NR
GWAS Catalog: GCST004950
Europe PMC: 25751625
 33,864 individuals European NR
GWAS Catalog: GCST004988
Europe PMC: 29059683
 139,274 individuals European NR
GWAS Catalog: GCST005075
Europe PMC: 29058716
 15,566 individuals European NR
GWAS Catalog: GCST005076
Europe PMC: 29058716
 72,261 individuals European NR
GWAS Catalog: GCST005077
Europe PMC: 29058716
 87,827 individuals European NR
GWAS Catalog: GCST000035
Europe PMC: 17529967
 754 individuals European NR
GWAS Catalog: GCST004948
Europe PMC: 19330027
 754 individuals European NR
GWAS Catalog: GCST007236
Europe PMC: 25751625
 89,677 individuals European NR
GWAS Catalog: GCST007302
Europe PMC: 23544012
 8,211 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
Europe PMC: 32991828
[
  • 1,264 cases
  • , 6,104 controls
]
 European MGI PheCode:174.1; ICD9CM:174.0, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233.0, V10.3; ICD10CM:C50, C50.0, C50.01, C50.011, C50.012, C50.019, C50.02, C50.021, C50.022, C50.029, C50.1, C50.11, C50.111, C50.112, C50.119, C50.12, C50.121, C50.122, C50.129, C50.2, C50.21, C50.211, C50.212, C50.219, C50.22, C50.221, C50.222, C50.229, C50.3, C50.31, C50.311, C50.312, C50.319, C50.32, C50.321, C50.322, C50.329, C50.4, C50.41, C50.411, C50.412, C50.419, C50.42, C50.421, C50.422, C50.429, C50.5, C50.51, C50.511, C50.512, C50.519, C50.52, C50.521, C50.522, C50.529, C50.6, C50.61, C50.611, C50.612, C50.619, C50.62, C50.621, C50.622, C50.629, C50.8, C50.81, C50.811, C50.812, C50.819, C50.82, C50.821, C50.822, C50.829, C50.9, C50.91, C50.911, C50.912, C50.919, C50.92, C50.921, C50.922, C50.929, D05, D05.0, D05.00, D05.01, D05.02, D05.1, D05.10, D05.11, D05.12, D05.8, D05.80, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92 — — — —

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
PPM001172 PSS000549|
European Ancestry|
7,785 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Breast cancer [female] OR: 1.488 [1.399, 1.582]
β: 0.397 (0.0313)		 AUROC: 0.607 [0.589, 0.623] Nagelkerke's Pseudo-R²: 0.0346
Brier score: 0.136
Odds Ratio (OR, top 1% vs. Rest): 3.06 [2.04, 4.6]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE174.1_GWAS-Catalog-r2019-05-03-X174.1_PT_MGI_20200608

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
PSS000549 PheCode:174.1; ICD9CM:174.0, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233.0, V10.3; ICD10CM:C50, C50.0, C50.01, C50.011, C50.012, C50.019, C50.02, C50.021, C50.022, C50.029, C50.1, C50.11, C50.111, C50.112, C50.119, C50.12, C50.121, C50.122, C50.129, C50.2, C50.21, C50.211, C50.212, C50.219, C50.22, C50.221, C50.222, C50.229, C50.3, C50.31, C50.311, C50.312, C50.319, C50.32, C50.321, C50.322, C50.329, C50.4, C50.41, C50.411, C50.412, C50.419, C50.42, C50.421, C50.422, C50.429, C50.5, C50.51, C50.511, C50.512, C50.519, C50.52, C50.521, C50.522, C50.529, C50.6, C50.61, C50.611, C50.612, C50.619, C50.62, C50.621, C50.622, C50.629, C50.8, C50.81, C50.811, C50.812, C50.819, C50.82, C50.821, C50.822, C50.829, C50.9, C50.91, C50.911, C50.912, C50.919, C50.92, C50.921, C50.922, C50.929, D05, D05.0, D05.00, D05.01, D05.02, D05.1, D05.10, D05.11, D05.12, D05.8, D05.80, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92 —
[
  • 1,341 cases
  • , 6,444 controls
]
 — European — MGI —