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(Variants and weights)

Polygenic Score (PGS) ID: PGS000015

Predicted Trait

Reported Trait: Breast cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): breast carcinoma

Score Details

Name: GPS_BC

Original Genome Build: hg19
Number of Variants: 5,218

PGS Development Method: Pruning and thresholding (P+T)
PGS Development Details/Relevant Parameters: r2 < 0.2; P < 5e−4; LD panel = 503 100G Europeans

Citation: Khera AV et al. Nat Genet (2018) | PGS Catalog Publication ID: PGP000006

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004988
PubMed: 29059683
139,274 individuals European
Score Development/Training
Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 codes (174 or 174.9) or ICD-10 codes (C50.X) in hospitalization records, or a breast cancer diagnosis reported to the national registry before the date of enrollment. 63,347 individuals
[ 2,576 cases, 65,923 controls]
0.0 % Male samples
European UKB UKB Phase 1

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000024 PSS000014 Khera AV et al. (2018) Reported Trait: Breast cancer cases AUROC: 0.69 [0.68 - 0.69] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.027 age; sex; Ancestry PC 1-4; genotyping chip

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000014 Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 codes (174 or 174.9) or ICD-10 codes (C50.X) in hospitalization records, or a breast cancer diagnosis reported to the national registry before the date of enrollment. 157,895 individuals
[ 6,586 cases, 164,481 controls]
0.0 % Male samples
European UKB UKB Phase 2