Polygenic Score (PGS) ID: PGS000028

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name PRS
Development Method
Name composite likelihood ratio
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)
Variants
Original Genome Build hg38
Number of Variants 83
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000018
Citation (link to publication) Shieh Y et al. Breast Cancer Res Treat (2016)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 80.7%
East Asian: 13.4%
Hispanic or Latin American: 3.3%
African: 2.6%
144,871 individuals (100%)
PGS Evaluation
East Asian: 33.3%
European: 33.3%
Multi-ancestry (including European): 33.3%
  • East Asian
  • European
  • Hispanic or Latin American
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002662
Europe PMC: 25327703
4,710 individuals Hispanic or Latin American NR
GWAS Catalog: GCST002346
Europe PMC: 2449363
6,225 individuals European NR
GWAS Catalog: GCST001930
Europe PMC: 23535733
39,387 individuals European NR
GWAS Catalog: GCST001420
Europe PMC: 22383897
5,242 individuals East Asian NR
GWAS Catalog: GCST002234
Europe PMC: 2414319
4,741 individuals East Asian NR
GWAS Catalog: GCST001683
Europe PMC: 22976474
3,748 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST001683
Europe PMC: 22976474
32,530 individuals European NR
GWAS Catalog: GCST002305
Europe PMC: 24325915
4,928 individuals European NR
GWAS Catalog: GCST001916
Europe PMC: 23544013
2,727 individuals European NR
GWAS Catalog: GCST000678
Europe PMC: 20453838
8,556 individuals European B58C, FBCS, POSH, UKBS
GWAS Catalog: GCST002537
Europe PMC: 25038754
9,450 individuals East Asian NR
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
PPM000056 PSS000040|
Multi-ancestry (including European)|
981 individuals
PGP000018 |
Shieh Y et al. Breast Cancer Res Treat (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
PPM000055 PSS000040|
Multi-ancestry (including European)|
981 individuals
PGP000018 |
Shieh Y et al. Breast Cancer Res Treat (2016)
Reported Trait: Breast cancer AUROC: 0.6 [0.57, 0.64]
PPM000060 PSS000039|
European Ancestry|
774 individuals
PGP000018 |
Shieh Y et al. Breast Cancer Res Treat (2016)
Reported Trait: Breast cancer AUROC: 0.63 [0.59, 0.67]
PPM000059 PSS000038|
East Asian Ancestry|
102 individuals
PGP000018 |
Shieh Y et al. Breast Cancer Res Treat (2016)
Reported Trait: Breast cancer AUROC: 0.62 [0.52, 0.73]

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
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.
[
  • 495 cases
  • , 486 controls
]
,
0.0 % Male samples
East Asian, European, Hispanic or Latin American CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.
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.
[
  • 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.
[
  • 387 cases
  • , 387 controls
]
,
0.0 % Male samples
European CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.