Publication: Breast cancer risk prediction using a clinical risk model and polygenic risk score.

Information

PGS Catalog Publication (PGP) ID: PGP000018
PubMed ID: 27565998
doi: 10.1007/s10549-016-3953-2

Publication Date: Aug. 26, 2016

Journal: Breast Cancer Res Treat

Authors: Shieh Y, Hu D, Ma L, Huntsman S, Gard CC, Leung JW, Tice JA, Vachon CM, Cummings SR, Kerlikowske K, Ziv E.

PGS Associated with PGP000018

PGS Developed By This Study

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 (PPM) ID Evaluated Score 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 PGS000028 (PRS) PSS000040 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.6 [0.57 - 0.64]
PPM000056 PGS000028 (PRS) 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
PPM000057 PGS000029 (PRS_AS) PSS000038 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.64 [0.53 - 0.74]
PPM000058 PGS000029 (PRS_AS) PSS000038 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
PPM000059 PGS000028 (PRS) PSS000038 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.62 [0.52 - 0.73]
PPM000060 PGS000028 (PRS) 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.