PGS Publication: PGP000018

Publication Information (EuropePMC)
Title Breast cancer risk prediction using a clinical risk model and polygenic risk score.
PubMed ID 27565998(Europe PMC)
doi 10.1007/s10549-016-3953-2
Publication Date Aug. 26, 2016
Journal Breast Cancer Res Treat
Author(s) Shieh Y, Hu D, Ma L, Huntsman S, Gard CC, Leung JW, Tice JA, Vachon CM, Cummings SR, Kerlikowske K, Ziv E.
Released in PGS: Oct. 14, 2019

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000028 PRS PGP000018
Shieh Y et al. Breast Cancer Res Treat (2016)
Breast cancer breast carcinoma 83 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000028/ScoringFiles/PGS000028.txt.gz
PGS000029 PRS_AS PGP000018
Shieh Y et al. Breast Cancer Res Treat (2016)
Breast cancer breast carcinoma 76 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000029/ScoringFiles/PGS000029.txt.gz

PGS 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)
Evaluated Score 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 PGS000028 (PRS) PSS000038 PGP000018
Shieh Y et al. (2016)
Reported Trait: Breast cancer AUROC: 0.62[0.52, 0.73]
PPM000060 PGS000028 (PRS) PSS000039 PGP000018
Shieh Y et al. (2016)
Reported Trait: Breast cancer AUROC: 0.63[0.59, 0.67]
PPM000055 PGS000028 (PRS) PSS000040 PGP000018
Shieh Y et al. (2016)
Reported Trait: Breast cancer AUROC: 0.6[0.57, 0.64]
PPM000056 PGS000028 (PRS) 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
PPM000057 PGS000029 (PRS_AS) PSS000038 PGP000018
Shieh Y et al. (2016)
Reported Trait: Breast cancer AUROC: 0.64[0.53, 0.74]
PPM000058 PGS000029 (PRS_AS) PSS000038 PGP000018
Shieh Y et al. (2016)
Reported Trait: Breast cancer AUROC: 0.72[0.62, 0.82] 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)
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
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.