PGS Publication: PGP000036

Publication Information (EuropePMC)
Title Addition of a polygenic risk score, mammographic density, and endogenous hormones to existing breast cancer risk prediction models: A nested case-control study.
PubMed ID 30180161(Europe PMC)
doi 10.1371/journal.pmed.1002644
Publication Date Sept. 4, 2018
Journal PLoS Med
Author(s) Zhang X, Rice M, Tworoger SS, Rosner BA, Eliassen AH, Tamimi RM, Joshi AD, Lindstrom S, Qian J, Colditz GA, Willett WC, Kraft P, Hankinson SE.
Released in PGS Catalog: Dec. 18, 2019

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

PGS Developed 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)
PGS000051
(PRS67)
 PGP000036 |
Zhang X et al. PLoS Med (2018)
 Breast cancer breast carcinoma 67
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000051/ScoringFiles/PGS000051.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
PPM000128 PGS000051
(PRS67)
 PSS000080|
Multi-ancestry (including European)|
11,880 individuals
 PGP000036 |
Zhang X et al. PLoS Med (2018)
 Reported Trait: Invasive breast cancer — AUROC: 0.65 [0.64, 0.66] — Gail BC risk model, Mammographic density (MD), Testoterone (T), estrone sulfate (E1S), prolactin (PRL) Age-adjusted AUC
PPM000130 PGS000051
(PRS67)
 PSS000080|
Multi-ancestry (including European)|
11,880 individuals
 PGP000036 |
Zhang X et al. PLoS Med (2018)
 Reported Trait: Invasive breast cancer — — Relative Risk (RR; higest vs. lowest quartile PRS): 2.5 [2.2, 2.8] Demographics and parameters of baseline blood draw (age, BMI, fasting status, time of day, season), history of benign breast disease, family history of breast cancer, age at menopause, age at menarche, physical activity, age at first birth and parity —
PPM000129 PGS000051
(PRS67)
 PSS000081|
Multi-ancestry (including European)|
8,160 individuals
 PGP000036 |
Zhang X et al. PLoS Med (2018)
 Reported Trait: Invasive breast cancer — AUROC: 0.678 [0.666, 0.69] — Rosner-Colditz BC risk model, Mammographic density (MD), Testoterone (T), estrone sulfate (E1S), prolactin (PRL) Age-adjusted AUC

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
PSS000080 Questionnaires were mailed to women biennially to collect information on breast cancer risk factors, including age at menarche, age at first birth, parity, family history of breast cancer, height, weight, physical activity, menopausal status, age at menopause, and HT use. Incident breast cancer cases up to 1 June 2010 were also identified through biennial questionnaires. Diagnoses were confirmed with the participants (or next of kin), and permission was obtained to collect relevant medical or pathology reports. Analysis was restricted to invasive breast cancer. Mean = 26.54 years
[
  • 4,006 cases
  • , 7,874 controls
]
,
0.0 % Male samples
 Mean = 53.7 years
Sd = 8.0 years
Range = [34.0, 70.0] years		 European, NR — NHS, NHS2 Performance metrics are reported for the "All women" results of Table 2
PSS000081 Questionnaires were mailed to women biennially to collect information on breast cancer risk factors, including age at menarche, age at first birth, parity, family history of breast cancer, height, weight, physical activity, menopausal status, age at menopause, and HT use. Incident breast cancer cases up to 1 June 2010 were also identified through biennial questionnaires. Diagnoses were confirmed with the participants (or next of kin), and permission was obtained to collect relevant medical or pathology reports. Analysis was restricted to invasive breast cancer. Mean = 23.08 years
[
  • 2,676 cases
  • , 5,484 controls
]
,
0.0 % Male samples
 Mean = 53.7 years
Sd = 8.0 years
Range = [34.0, 70.0] years		 European, NR — NHS, NHS2 Performance metrics are reported for the "All women" results of Table 3