PGS Publication: PGP000625

Publication Information (EuropePMC)
Title Validation of the BOADICEA model and a 313-variant polygenic risk score for breast cancer risk prediction in a Dutch prospective cohort.
PubMed ID 32624571(Europe PMC)
doi 10.1038/s41436-020-0884-4
Publication Date July 6, 2020
Journal Genet Med
Author(s) Lakeman IMM, Rodríguez-Girondo M, Lee A, Ruiter R, Stricker BH, Wijnant SRA, Kavousi M, Antoniou AC, Schmidt MK, Uitterlinden AG, van Rooij J, Devilee P.
Released in PGS Catalog: May 8, 2024

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000004
(PRS313_BC)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Breast cancer breast carcinoma 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.txt.gz

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) 		Evaluated Score 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
PPM021285 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer HR: 1.56 [1.4, 1.74] — — Age at inclusion in the Rotterdam Study —
PPM021286 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer in women below the age of 50 HR: 2.74 [1.72, 4.37] — — Age at inclusion in the Rotterdam Study —
PPM021287 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer in women aged between 50 and 75 HR: 1.74 [1.52, 2.0] — — Age at inclusion in the Rotterdam Study —
PPM021288 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer in women above the age of 75 HR: 1.29 [1.08, 1.55] — — Age at inclusion in the Rotterdam Study —
PPM021289 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident invasive breast cancer HR: 1.57 [1.4, 1.77] — — Age at inclusion in the Rotterdam Study —
PPM021290 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident in situ breast cancer HR: 1.43 [1.01, 2.01] — — Age at inclusion in the Rotterdam Study —
PPM021291 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer in women below the age of 60 — C-index: 0.632 [0.58, 0.69] — — —
PPM021292 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer in women aged between the ages of 60 and 70 — C-index: 0.673 [0.61, 0.73] — — —
PPM021293 PGS000004
(PRS313_BC)
 PSS011678|
European Ancestry|
6,522 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer in women aged 70 or above — C-index: 0.562 [0.48, 0.62] — — —
PPM021294 PGS000004
(PRS313_BC)
 PSS011677|
European Ancestry|
4,377 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer — C-index: 0.636 [0.59, 0.68] — Age at inclusion in the Rotterdam Study Calculated using the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICIEA)
PPM021295 PGS000004
(PRS313_BC)
 PSS011677|
European Ancestry|
4,377 individuals
 PGP000625 |
Lakeman IMM et al. Genet Med (2020)
|Ext.		 Reported Trait: Incident breast cancer — C-index: 0.653 [0.6, 0.7] — Age at inclusion in the Rotterdam Study, age at menarche, age at menopause, number of children, age at first live birth, use of oral contraception, use of hormone replacement therapy, body mass index (BMI), height, alcohol use Calculated using the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICIEA)

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
PSS011677 Cases include women that developed breast cancer. All women were below the age of 70. Median = 10.0 years
Range = [0.03, 10.0] years
[
  • 163 cases
  • , 4,214 controls
]
,
0.0 % Male samples
 Mean = 59.92 years European
(Dutch)		 — RS —
PSS011678 Cases include women that developed breast cancer. Within the cases there were 290 invasive breast cancer cases and 34 in situ breast cancer cases. Median = 12.4 years
Range = [0.03, 24.43] years
[
  • 320 cases
  • , 6,202 controls
]
,
0.0 % Male samples
 Mean = 66.05 years European
(Dutch)		 — RS —