Polygenic Score (PGS) ID: PGS004069

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
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Score Details

Score Construction
PGS Name megaprs.CV.GCST004988.Breast_cancer
Development Method
Name megaprs.CV
Parameters Model:Model173,Type:bayesr,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:NA,Bolt_f2:NA,BayesR_p1:0.78,BayesR_p2:0.2,BayesR_p3:0.02,BayesR_p4:0
Variants
Original Genome Build GRCh38
Number of Variants 869,407
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)
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
— 12,483 individuals,
0.0 % Male samples
 European UKB — — — — —

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
PPM019407 PSS011215|
European Ancestry|
130,758 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Breast cancer OR: 1.64103 [1.57912878, 1.70535148]
β: 0.49532 [0.45687329, 0.53377123]		 AUROC: 0.63737 [0.62675736, 0.64797822] R²: 0.0532 [0.04622562, 0.06191163] 0 beta = log(or)/sd_pgs
PPM019408 PSS011227|
European Ancestry|
217,530 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Breast cancer OR: 1.7432 [1.71450629, 1.77238361]
β: 0.55573 [0.53912516, 0.57232531]		 AUROC: 0.65242 [0.6480568, 0.65678307] R²: 0.06545 [0.06174367, 0.06888215] 0 beta = log(or)/sd_pgs
PPM019409 PSS011238|
South Asian Ancestry|
24,319 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Breast cancer OR: 1.56536 [1.35914439, 1.80285464]
β: 0.44811 [0.30685538, 0.58937132]		 AUROC: 0.62314 [0.58448319, 0.66179346] R²: 0.03515 [0.01639285, 0.06168013] 0 beta = log(or)/sd_pgs
PPM019410 PSS011254|
European Ancestry|
35,377 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Breast cancer OR: 1.72445 [1.64139537, 1.81169954]
β: 0.54491 [0.49554672, 0.59426538]		 AUROC: 0.64679 [0.63364992, 0.65993923] R²: 0.06355 [0.05288965, 0.07449614] 0 beta = log(or)/sd_pgs
PPM019411 PSS011282|
South Asian Ancestry|
4,350 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Breast cancer OR: 1.51041 [1.305849, 1.74702266]
β: 0.41238 [0.2668534, 0.557913]		 AUROC: 0.61087 [0.57033984, 0.65140365] R²: 0.02956 [0.01317004, 0.05393655] 0 beta = log(or)/sd_pgs
PPM019412 PSS011268|
European Ancestry|
48,968 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Breast cancer OR: 1.78417 [1.71851145, 1.85232925]
β: 0.57895 [0.54145848, 0.6164439]		 AUROC: 0.65585 [0.64609462, 0.66560523] R²: 0.07087 [0.06226027, 0.0800237] 0 beta = log(or)/sd_pgs

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
PSS011215 — —
[
  • 2,685 cases
  • , 128,073 controls
]
,
0.0 % Male samples
 — European — EB —
PSS011282 — —
[
  • 196 cases
  • , 4,154 controls
]
,
0.0 % Male samples
 — South Asian — UKB —
PSS011254 — —
[
  • 1,729 cases
  • , 33,648 controls
]
,
0.0 % Male samples
 — European — HUNT —
PSS011227 C3_BREAST, ICD10: C0, ICD9: 174 —
[
  • 16,076 cases
  • , 201,454 controls
]
,
0.0 % Male samples
 — European — FinnGen —
PSS011268 — —
[
  • 3,120 cases
  • , 45,848 controls
]
,
0.0 % Male samples
 — European — UKB —
PSS011238 — —
[
  • 197 cases
  • , 24,122 controls
]
,
0.0 % Male samples
 — South Asian — G&H —