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 Catalog: Oct. 14, 2019

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

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

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) 		Evaluated Score 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 PGS000028
(PRS)
 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
PPM000058 PGS000029
(PRS_AS)
 PSS000038|
East Asian Ancestry|
102 individuals
 PGP000018 |
Shieh Y et al. Breast Cancer Res Treat (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
PPM000055 PGS000028
(PRS)
 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 PGS000028
(PRS)
 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 PGS000028
(PRS)
 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] — — —
PPM000057 PGS000029
(PRS_AS)
 PSS000038|
East Asian Ancestry|
102 individuals
 PGP000018 |
Shieh Y et al. Breast Cancer Res Treat (2016)
 Reported Trait: Breast cancer — AUROC: 0.64 [0.53, 0.74] — — —

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.