Polygenic Score (PGS) ID: PGS000052

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Dec. 18, 2019
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Score Details

Score Construction
PGS Name sPRS161
Variants
Original Genome Build GRCh37
Number of Variants 161
Development Method
Name Genome-wide significant SNPs
Parameters p<5x10−8
PGS Source
PGS Catalog Publication (PGP) ID PGP000037
Citation (link to publication) Lakeman IMM et al. J Med Genet (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
Score Development/Training
European: 100%
684 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004988
Europe PMC: 29059683
139,274 individuals European
Score Development/Training
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
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.
[
  • 357 cases
  • , 327 controls
]
,
0.0 % Male samples
Mean (Cases) = 56.0 years
Sd (Cases) = 10.0 years
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 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
PPM000131 PSS000082|
European Ancestry|
585 individuals
PGP000037 |
Lakeman IMM et al. J Med Genet (2019)
Reported Trait: breast cancer HR: 1.16 [1.03, 1.28] family history (estimated using the BOADICEA risk model)

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
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.
[
  • 323 cases
  • , 262 controls
]
,
0.0 % Male samples
Mean (Cases) = 51.0 years
Sd (Cases) = 11.0 years
European