Polygenic Score (PGS) ID: PGS000783

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: May 28, 2021
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Score Details

Score Construction
PGS Name CC_Breast_IV
Development Method
Name 162 variants from Graff et al (PGS000072) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 162
Effect Weight Type Inverse-variance weighting
PGS Source
PGS Catalog Publication (PGP) ID PGP000186
Citation (link to publication) Kachuri L 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
PPM002054 PSS001011|
European Ancestry|
216,273 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident breast cancer HR: 1.52 [1.47, 1.56] AUROC: 0.637
C-index: 0.635 (0.004)		 R²: 0.146 Age at assessment, family history of breast cancer, genotyping array, PCs(1-15), parity( ≥1 live birth vs. none), age at menarche, body mass index, menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use, alcool intake, (Body mass index)*(menopausal status) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002070 PSS001011|
European Ancestry|
216,273 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident breast cancer — AUROC: 0.626
C-index: 0.62 (0.005)		 R²: 0.122 Age, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS001011 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 4,760 cases
  • , 211,513 controls
]
,
0.0 % Male samples
 — European — UKB —