Polygenic Score (PGS) ID: PGS004083

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Dec. 19, 2023
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name prscs.auto.GCST004988.Breast_cancer
Development Method
Name PRS-CS-auto
Parameters phi:auto
Variants
Original Genome Build GRCh38
Number of Variants 1,103,877
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
Score Development/Training
European: 100%
12,483 individuals (100%)
PGS Evaluation
European: 66.7%
South Asian: 33.3%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST004988
Europe PMC: 29059683
139,274 individualsEuropeanNR
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Score Development/Training
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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
—12,483 individuals,
0.0 % Male samples
EuropeanUKB—————
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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.

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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
PPM019419PSS011215|
European Ancestry|
130,758 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Breast cancerβ: 0.48736 [0.44905474, 0.52567252]
OR: 1.62802 [1.56683043, 1.69159609]		AUROC: 0.63532 [0.62467241, 0.64596639]R²: 0.05189 [0.04462939, 0.06050746]0beta = log(or)/sd_pgs
PPM019420PSS011227|
European Ancestry|
217,530 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Breast cancerOR: 1.73797 [1.70945914, 1.76696055]
β: 0.55272 [0.53617703, 0.56926087]		AUROC: 0.65207 [0.64770258, 0.65644351]R²: 0.06524 [0.06134318, 0.06889406]0beta = log(or)/sd_pgs
PPM019421PSS011238|
South Asian Ancestry|
24,319 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Breast cancerOR: 1.57454 [1.3683506, 1.81179039]
β: 0.45396 [0.31360607, 0.59431552]		AUROC: 0.62734 [0.58839198, 0.66629096]R²: 0.0365 [0.01640351, 0.06192232]0beta = log(or)/sd_pgs
PPM019422PSS011254|
European Ancestry|
35,377 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Breast cancerOR: 1.72094 [1.6384216, 1.80760485]
β: 0.54287 [0.49373334, 0.59200268]		AUROC: 0.64671 [0.63347915, 0.65993367]R²: 0.06366 [0.05229169, 0.07516806]0beta = log(or)/sd_pgs
PPM019423PSS011282|
South Asian Ancestry|
4,350 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Breast cancerOR: 1.51133 [1.30438605, 1.7511135]
β: 0.41299 [0.26573247, 0.56025187]		AUROC: 0.61379 [0.57261519, 0.65495499]R²: 0.029 [0.01275949, 0.05212183]0beta = log(or)/sd_pgs
PPM019424PSS011268|
European Ancestry|
48,968 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Breast cancerOR: 1.77492 [1.70965861, 1.84266319]
β: 0.57375 [0.5362937, 0.61121191]		AUROC: 0.65535 [0.64554283, 0.66515647]R²: 0.06966 [0.06127445, 0.07856851]0beta = log(or)/sd_pgs
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Evaluated Samples

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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
PSS011215——
[
  • 2,685 cases
  • , 128,073 controls
]
,
0.0 % Male samples
—European—EB—
PSS011227C3_BREAST, ICD10: C0, ICD9: 174—
[
  • 16,076 cases
  • , 201,454 controls
]
,
0.0 % Male samples
—European—FinnGen—
PSS011238——
[
  • 197 cases
  • , 24,122 controls
]
,
0.0 % Male samples
—South Asian—G&H—
PSS011254——
[
  • 1,729 cases
  • , 33,648 controls
]
,
0.0 % Male samples
—European—HUNT—
PSS011268——
[
  • 3,120 cases
  • , 45,848 controls
]
,
0.0 % Male samples
—European—UKB—
PSS011282——
[
  • 196 cases
  • , 4,154 controls
]
,
0.0 % Male samples
—South Asian—UKB—
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