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(Variants and weights)

Polygenic Score (PGS) ID: PGS000051

Predicted Trait

Reported Trait: Breast Cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): breast carcinoma

Score Details

Name: PRS67

Original Genome Build: GRCh36
Number of Variants: 67

PGS Development Method: Hard thresholding
PGS Development Details/Relevant 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]

Citation: Zhang X et al. PLoS Med (2018) | PGS Catalog Publication ID: PGP000036

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001937
PubMed: 23535729
22,627 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000128 PSS000080 Zhang X et al. (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
PPM000129 PSS000081 Zhang X et al. (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
PPM000130 PSS000080 Zhang X et al. (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

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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. 11,880 individuals
[ 4,006 cases, 7,874 controls]
0.00 %% Male samples
Other The study population was described as “predominantly white” [PGS Catalog Broad Ancestral Category: European] NHS2, NHS 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. 8,160 individuals
[ 2,676 cases, 5,484 controls]
0.00 %% Male samples
Other The study population was described as “predominantly white” [PGS Catalog Broad Ancestral Category: European] NHS2, NHS Performance metrics are reported for the "All women" results of Table 3