PGS Publication: PGP000033

Publication Information (EuropePMC)
Title Evaluation of Polygenic Risk Scores for Breast and Ovarian Cancer Risk Prediction in BRCA1 and BRCA2 Mutation Carriers.
PubMed ID 28376175(Europe PMC)
doi 10.1093/jnci/djw302
Publication Date July 1, 2017
Journal J Natl Cancer Inst
Author(s) Kuchenbaecker KB, McGuffog L, Barrowdale D, Lee A, Soucy P, Dennis J, Domchek SM, Robson M, Spurdle AB, Ramus SJ, Mavaddat N, Terry MB, Neuhausen SL, Schmutzler RK, Simard J, Pharoah PDP, Offit K, Couch FJ, Chenevix-Trench G, Easton DF, Antoniou AC.
Released in PGS: Dec. 18, 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)
PGS000045 BCPRS_Overall PGP000033
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
Breast cancer breast carcinoma 88 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000045/ScoringFiles/PGS000045.txt.gz
PGS000046 BCPRS_ER+ PGP000033
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
Estrogen receptor [ER]-positive breast cancer estrogen-receptor positive breast cancer 87 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000046/ScoringFiles/PGS000046.txt.gz
PGS000047 BCPRS_ER- PGP000033
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
Estrogen receptor [ER]-negative breast cancer estrogen-receptor negative breast cancer 53 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000047/ScoringFiles/PGS000047.txt.gz
PGS000048 OCPRS_Overall PGP000033
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
Ovarian cancer ovarian carcinoma 17 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000048/ScoringFiles/PGS000048.txt.gz

External PGS Evaluated 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)
PGS000001 PRS77_BC PGP000001
Mavaddat N et al. J Natl Cancer Inst (2015)
Breast Cancer breast carcinoma 77 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz
PGS000002 PRS77_ERpos PGP000001
Mavaddat N et al. J Natl Cancer Inst (2015)
ER-positive Breast Cancer estrogen-receptor positive breast cancer 77 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000002/ScoringFiles/PGS000002.txt.gz
PGS000003 PRS77_ERneg PGP000001
Mavaddat N et al. J Natl Cancer Inst (2015)
ER-negative Breast Cancer estrogen-receptor negative breast cancer 77 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000003/ScoringFiles/PGS000003.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
PPM000106 PGS000045 (BCPRS_Overall) PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.14[1.11, 1.17] C-index: 0.541[0.53, 0.551] Country, birth year
PPM000107 PGS000045 (BCPRS_Overall) PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22[1.17, 1.28] C-index: 0.566[0.551, 0.581] Country, birth year
PPM000108 PGS000046 (BCPRS_ER+) PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.11[1.08, 1.15] C-index: 0.532[0.522, 0.543] Country, birth year
PPM000109 PGS000046 (BCPRS_ER+) PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22[1.16, 1.27] C-index: 0.566[0.551, 0.581] Country, birth year
PPM000110 PGS000047 (BCPRS_ER-) PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.27[1.23, 1.31] C-index: 0.581[0.571, 0.592] Country, birth year
PPM000111 PGS000047 (BCPRS_ER-) PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.15[1.1, 1.2] C-index: 0.538[0.523, 0.553] Country, birth year
PPM000112 PGS000048 (OCPRS_Overall) PSS000072 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Ovarian cancer in BRCA1 mutation carriers HR: 1.28[1.22, 1.34] C-index: 0.579[0.559, 0.6] Country, birth year
PPM000113 PGS000048 (OCPRS_Overall) PSS000073 PGP000033
Kuchenbaecker KB et al. (2017)
Reported Trait: Ovarian cancer in BRCA2 mutation carriers HR: 1.49[1.34, 1.65] C-index: 0.628[0.592, 0.665] Country, birth year
PPM000114 PGS000001 (PRS77_BC) PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.13[1.1, 1.16] Country, birth year
PPM000115 PGS000002 (PRS77_ERpos) PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.09[1.06, 1.12] Country, birth year
PPM000116 PGS000003 (PRS77_ERneg) PSS000070 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.24[1.21, 1.28] Country, birth year
PPM000117 PGS000001 (PRS77_BC) PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22[1.17, 1.28] Country, birth year
PPM000118 PGS000002 (PRS77_ERpos) PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22[1.17, 1.27] Country, birth year
PPM000119 PGS000003 (PRS77_ERneg) PSS000071 PGP000033
Kuchenbaecker KB et al. (2017)
Ext.
Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.13[1.08, 1.18] Country, birth year

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
PSS000072 BRCA1 mutation carriers were followed until the age of ovarian cancer diagnosis, age at risk-reducing salpingo-oophorectomy (RRSO) or age at last observation. Breast cancer diagnosis was not considered as a censoring event in the ovarian cancer analysis
[
  • 2,462 cases
  • , 12,790 controls
]
,
0.0 % Male samples
European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 50
PSS000073 BRCA2 mutation carriers were followed until the age of ovarian cancer diagnosis, age at risk-reducing salpingo-oophorectomy (RRSO) or age at last observation. Breast cancer diagnosis was not considered as a censoring event in the ovarian cancer analysis
[
  • 631 cases
  • , 7,580 controls
]
,
0.0 % Male samples
European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 57
PSS000070 BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first.
[
  • 7,797 cases
  • , 7,455 controls
]
,
0.0 % Male samples
European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 40
PSS000071 BRCA2 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first.
[
  • 4,330 cases
  • , 3,881 controls
]
,
0.0 % Male samples
European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 43