Polygenic Score (PGS) ID: PGS000153

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: April 29, 2020
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Score Details

Score Construction
PGS Name cGRS_Breast
Development Method
Name Pruning and Thresholding (P+T)
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
Variants
Original Genome Build NR
Number of Variants 66
Effect Weight Type Odds Ratio over expected risk
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
102,721 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: GCST003842
Europe PMC: 27117709
 19,291 individuals European NR
GWAS Catalog: GCST003845
Europe PMC: 27117709
 19,291 individuals European NR
GWAS Catalog: GCST004950
Europe PMC: 25751625
 33,864 individuals European NR
GWAS Catalog: GCST000162
Europe PMC: 18326623
 548 individuals European NR
GWAS Catalog: GCST000035
Europe PMC: 17529967
 754 individuals European NR
GWAS Catalog: GCST000952
Europe PMC: 2126313
 6,346 individuals European NR
GWAS Catalog: GCST001937
Europe PMC: 23535729
 22,627 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
PPM000484 PSS000273|
European Ancestry|
7,847 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Breast cancer — — Odds Ratio (OR; high vs. average risk groups): 1.47 [1.23, 1.76] — —
PPM000473 PSS000273|
European Ancestry|
7,847 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Breast cancer — — Mean realative risk: 1.15 [1.11, 1.2]
Wilcoxon test (case vs. control) p-value: 1.48e-14		 — —

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
PSS000273 Primary tumor samples from TCGA —
[
  • 827 cases
  • , 0 controls
]
,
0.0 % Male samples
 Mean = 60.0 years
Sd = 13.0 years		 European — TCGA —
PSS000273 — —
[
  • 0 cases
  • , 7,020 controls
]
,
0.0 % Male samples
 — European — eMERGE —