PGS Publication: PGP000247

Publication Information (EuropePMC)
Title Genomic Risk Prediction for Breast Cancer in Older Women.
PubMed ID 34298747(Europe PMC)
doi 10.3390/cancers13143533
Publication Date July 14, 2021
Journal Cancers (Basel)
Author(s) Lacaze P, Bakshi A, Riaz M, Orchard SG, Tiller J, Neumann JT, Carr PR, Joshi AD, Cao Y, Warner ET, Manning A, Nguyen-Dumont T, Southey MC, Milne RL, Ford L, Sebra R, Schadt E, Gately L, Gibbs P, Thompson BA, Macrae FA, James P, Winship I, McLean C, Zalcberg JR, Woods RL, Chan AT, Murray AM, McNeil JJ.
Released in PGS Catalog: Nov. 4, 2021

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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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
PPM005148 PGS000004
(PRS313_BC)
 PSS003595|
European Ancestry|
6,339 individuals
 PGP000247 |
Lacaze P et al. Cancers (Basel) (2021)
|Ext.		 Reported Trait: Incident invasive estrogen receptor postivie/progesterone receptor positive breast cancer HR: 1.53 [1.22, 1.91] — — Family history of breast cancer (first-degree blood relatives), treatment (asprin/placebo), age at enrolment, number of children, alcohol use, body mass index at enrolment, use of hormone replacement therapy at enrolment Only 271 SNPs from PGS000004 were utilised. 42 SNPs were not included due to low imputation quality scores (r^2 < 0.3).
PPM005150 PGS000004
(PRS313_BC)
 PSS003595|
European Ancestry|
6,339 individuals
 PGP000247 |
Lacaze P et al. Cancers (Basel) (2021)
|Ext.		 Reported Trait: Diagnosis of prevalent invasive breast cancer before the age of 50 OR: 1.39 [1.08, 1.8] — — Family history of breast cancer (first-degree blood relatives) Only 271 SNPs from PGS000004 were utilised. 42 SNPs were not included due to low imputation quality scores (r^2 < 0.3).
PPM005151 PGS000004
(PRS313_BC)
 PSS003595|
European Ancestry|
6,339 individuals
 PGP000247 |
Lacaze P et al. Cancers (Basel) (2021)
|Ext.		 Reported Trait: Diagnosis of prevalent invasive breast cancer at the age of 50 or over OR: 1.47 [1.33, 1.63] — — Family history of breast cancer (first-degree blood relatives) Only 271 SNPs from PGS000004 were utilised. 42 SNPs were not included due to low imputation quality scores (r^2 < 0.3).
PPM005147 PGS000004
(PRS313_BC)
 PSS003595|
European Ancestry|
6,339 individuals
 PGP000247 |
Lacaze P et al. Cancers (Basel) (2021)
|Ext.		 Reported Trait: Incident invasive breast cancer HR: 1.43 [1.18, 1.73] C-index: 0.65 [0.59, 0.71] Hazard Ratio (HR, top 20% vs bottom 20%): 2.16 [1.21, 3.86] Family history of breast cancer (first-degree blood relatives), treatment (asprin/placebo), age at enrolment, number of children, alcohol use, body mass index at enrolment, use of hormone replacement therapy at enrolment Only 271 SNPs from PGS000004 were utilised. 42 SNPs were not included due to low imputation quality scores (r^2 < 0.3).
PPM005149 PGS000004
(PRS313_BC)
 PSS003595|
European Ancestry|
6,339 individuals
 PGP000247 |
Lacaze P et al. Cancers (Basel) (2021)
|Ext.		 Reported Trait: Prevalent invasive breast cancer OR: 1.47 [1.34, 1.61] AUROC: 0.62 [0.59, 0.65] Odds Ratio (OR, top 20% vs bottom 20%): 3.16 [2.26, 4.49] Family history of breast cancer (first-degree blood relatives), pathogenic variants in breast cancer-associated genes Only 271 SNPs from PGS000004 were utilised. 42 SNPs were not included due to low imputation quality scores (r^2 < 0.3).

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
PSS003595 Cases were individuals with invasive breast cancer. Of the 585 cases, 475 were individuals with prevalent invasive breast cancer whilst 110 were individuals with incident invasive breast cancer. Incident invasive breast cancer was adjudicated by an expert panel using histopathology, metastasis imaging or other clinical evidence. Histopathology was available for 103 of the 110 individuals with incident invasive breast cancer. Of the 103 individuals, 74 had incident invasive estrogren receptor postivie/progesterone receptor positive breast cancer. Age at diagnosis of prevalent invasive breast cancer was self-reported as before or after 50 years. Of the 475 individuals with prevalent invasive breast cancer 60 had been diagnosed before the age of 50, whilst the remaining 415 had been diagnosed at age 50 or over. Median = 4.7 years
IQR = [3.65, 5.75] years
[
  • 585 cases
  • , 5,754 controls
]
,
0.0 % Male samples
 Mean = 75.1 years European — ASPREE —