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(Variants and weights)

Polygenic Score (PGS) ID: PGS000028

Predicted Trait

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

Score Details

Name: PRS

Original Genome Build: hg38
Number of Variants: 83

PGS Development Method: composite likelihood ratio
PGS Development Details/Relevant Parameters: SNPs with p<5x10-8 in studies of invasive breast cancer in Caucasian, Asian, or Hispanic populations, or proxy SNP on Illumina Oncoarray in strong LD (r2>0.9)

Citation: Shieh Y et al. Breast Cancer Res Treat (2016) | PGS Catalog Publication ID: PGP000018

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002537
PubMed: 25038754
9,450 individuals East Asian
GWAS Catalog: GCST002662
PubMed: 25327703
4,710 individuals Hispanic or Latin American
GWAS Catalog: GCST002346
PubMed: 24493630
6,225 individuals European
GWAS Catalog: GCST001930
PubMed: 23535733
39,387 individuals European
GWAS Catalog: GCST001420
PubMed: 22383897
5,242 individuals East Asian
GWAS Catalog: GCST002234
PubMed: 24143190
4,741 individuals East Asian
GWAS Catalog: GCST001683
PubMed: 22976474
32,530 individuals European
GWAS Catalog: GCST001683
PubMed: 22976474
3,748 individuals African American or Afro-Caribbean
GWAS Catalog: GCST001937
PubMed: 23535729
22,627 individuals European
GWAS Catalog: GCST002305
PubMed: 24325915
4,928 individuals European
GWAS Catalog: GCST001916
PubMed: 23544013
2,727 individuals European
GWAS Catalog: GCST000678
PubMed: 20453838
8,556 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
PPM000055 PSS000040 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.6 [0.57 - 0.64]
PPM000056 PSS000040 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.65 [0.61 - 0.68] BCSC risk model BCSC risk model includes mammographic breast density, age, ethnicity, first-degree relative with breast cancer, and history of breast biopsy
PPM000059 PSS000038 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.62 [0.52 - 0.73]
PPM000060 PSS000039 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.63 [0.59 - 0.67]

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
PSS000038 Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. 102 individuals
[ 51 cases, 51 controls]
0.0 % Male samples
East Asian CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.
PSS000039 Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. 774 individuals
[ 387 cases, 387 controls]
0.0 % Male samples
European CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.
PSS000040 Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. 981 individuals
[ 495 cases, 486 controls]
0.0 % Male samples
Other Cohort contains individuals of East Asian, European & Hispanic ancestries CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.