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(Variants and weights)

Polygenic Score (PGS) ID: PGS000052

Predicted Trait

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

Score Details

Name: sPRS161

Original Genome Build: GRCh37
Number of Variants: 161

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: p<5x10−8

Citation: Lakeman IMM et al. J Med Genet (2019) | PGS Catalog Publication ID: PGP000037

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
Incident breast cancer cases, not selected for breast cancer family history enrolled between 1996 and 2006 from the Oorsprong van borstkanker integraal onderzocht (ORIGO) study. 327 healthy genotyped bloodbank donors were included in the ORIGO cohort as controls. 684 individuals
[ 357 cases, 327 controls]
0.00 %% Male samples
European ORIGO Used to study the mean and standard deviation (SD) of the sPRS

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
PPM000131 PSS000082 Lakeman IMM et al. (2019) Reported Trait: breast cancer HR: 1.16 [1.03 - 1.28] family history (estimated using the BOADICEA risk model)

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
PSS000082 A family-based cohort including 323 breast cancer cases and 262 unaffected relatives from 101 families. Unaffected relatives derived from 49 out of 101 families. 585 individuals
[ 323 cases, 262 controls]
0.00 %% Male samples
European