Polygenic Score (PGS) ID: PGS002242

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: April 13, 2022
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Terms and Licenses
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Score Details

Score Construction
PGS Name ldpred_breastcancer
Development Method
Name LDpred
Parameters p = 0.03, LD radius = 2000, LD reference panel: European ancestry in 1000 Genomes
Variants
Original Genome Build GRCh37
Number of Variants 6,494,889
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000271
Citation (link to publication) Mars N et al. Cell Genom (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
Score Development/Training
European: 100%
175,364 individuals (100%)
PGS Evaluation
European: 55.6%
African: 22.2%
East Asian: 11.1%
South Asian: 11.1%
9 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
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 7,349 cases
  • , 168,015 controls
]
 European
(Finnish)		 FinnGen — — — — —

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
PPM012734 PSS009523|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.48 [1.45, 1.51] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012738 PSS009519|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.45 [1.37, 1.53] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012742 PSS009515|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.25 [1.21, 1.28] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012746 PSS009527|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.5 [1.43, 1.58] — — birth year, 10 PCs (+/- dataset-specific technical covariates) —
PPM012750 PSS009535|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.45 [1.38, 1.54] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012754 PSS009531|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 0.9 [0.69, 1.17] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012758 PSS009543|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.5 [1.47, 1.53] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012763 PSS009539|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.12 [0.93, 1.35] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012768 PSS009547|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.47 [1.23, 1.75] — — age, 10 PCs (+/- dataset-specific technical covariates) —

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
PSS009535 — —
[
  • 1,513 cases
  • , 24,183 controls
]
,
0.0 % Male samples
 — European — MGBB —
PSS009539 — —
[
  • 132 cases
  • , 7,486 controls
]
,
0.0 % Male samples
 — African unspecified — UKB —
PSS009543 — —
[
  • 11,075 cases
  • , 332,601 controls
]
,
0.0 % Male samples
 — European British UKB —
PSS009515 — —
[
  • 5,316 cases
  • , 173,410 controls
]
,
0.0 % Male samples
 — East Asian
(Japanese)		 — BBJ —
PSS009547 — —
[
  • 139 cases
  • , 7,489 controls
]
,
0.0 % Male samples
 — South Asian — UKB —
PSS009519 — —
[
  • 1,379 cases
  • , 109,218 controls
]
,
0.0 % Male samples
 — European
(Estonian)		 — EB —
PSS009523 — —
[
  • 11,573 cases
  • , 246,829 controls
]
,
0.0 % Male samples
 — European
(Finnish)		 — FinnGen —
PSS009527 — —
[
  • 1,731 cases
  • , 67,691 controls
]
,
0.0 % Male samples
 — European Norwegian HUNT —
PSS009531 — —
[
  • 64 cases
  • , 1,471 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean — MGBB —