Polygenic Score (PGS) ID: PGS000051

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Dec. 18, 2019
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Score Details

Score Construction
PGS Name PRS67
Development Method
Name Hard thresholding
Parameters 41 SNPs were identified with P<5xE-08 and additional 26 SNPs were further identified through familiar risk fitted disctribution of z scores in those SNPs that did not have associations reaching genome-wide levels of significance [ refer to Overall contribution to breast cancer susceptibility section of reference 8, Michailidou et al 2014]
Variants
Original Genome Build NR
Number of Variants 67
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000036
Citation (link to publication) Zhang X et al. PLoS Med (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
22,627 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • Not Reported
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001937
Europe PMC: 23535729
 22,627 individuals European NR

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
PPM000128 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 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 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