Polygenic Score (PGS) ID: PGS000028

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

Score Details

Score Construction
PGS Name PRS
Variants
Original Genome Build hg38
Number of Variants 83
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)
PGS Source
PGS Catalog Publication (PGP) ID PGP000018
Citation (link to publication) Shieh Y et al. Breast Cancer Res Treat (2016)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001420
EuropePMC: 22383897
5,242 individuals East Asian
GWAS Catalog: GCST002537
EuropePMC: 25038754
9,450 individuals East Asian
GWAS Catalog: GCST001930
EuropePMC: 23535733
39,387 individuals European
GWAS Catalog: GCST002234
EuropePMC: 2414319
4,741 individuals East Asian
GWAS Catalog: GCST001683
EuropePMC: 22976474
3,748 individuals African American or Afro-Caribbean
GWAS Catalog: GCST001683
EuropePMC: 22976474
32,530 individuals European
GWAS Catalog: GCST001937
EuropePMC: 23535729
22,627 individuals European
GWAS Catalog: GCST002305
EuropePMC: 24325915
4,928 individuals European
GWAS Catalog: GCST001916
EuropePMC: 23544013
2,727 individuals European
GWAS Catalog: GCST000678
EuropePMC: 20453838
8,556 individuals European
GWAS Catalog: GCST002662
EuropePMC: 25327703
4,710 individuals Hispanic or Latin American
GWAS Catalog: GCST002346
EuropePMC: 2449363
6,225 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 ID
(PPM ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000059 PSS000038 PGP000018
Shieh Y et al. (2016)
Reported Trait: Breast cancer AUROC: 0.62[0.52, 0.73]
PPM000060 PSS000039 PGP000018
Shieh Y et al. (2016)
Reported Trait: Breast cancer AUROC: 0.63[0.59, 0.67]
PPM000055 PSS000040 PGP000018
Shieh Y et al. (2016)
Reported Trait: Breast cancer AUROC: 0.6[0.57, 0.64]
PPM000056 PSS000040 PGP000018
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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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
Other Cohort contains individuals of East Asian, European & Hispanic ancestries 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.