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 Catalog: Dec. 18, 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)
PGS000045
(BCPRS_Overall)
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
 Breast cancer breast carcinoma 88
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000045/ScoringFiles/PGS000045.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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000047/ScoringFiles/PGS000047.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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000046/ScoringFiles/PGS000046.txt.gz
PGS000048
(OCPRS_Overall)
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
 Ovarian cancer ovarian carcinoma 17
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000048/ScoringFiles/PGS000048.txt.gz

External PGS Evaluated 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)
PGS000001
(PRS77_BC)
 PGP000001 |
Mavaddat N et al. J Natl Cancer Inst (2015)
 Breast cancer breast carcinoma 77
-
 https://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
-
 https://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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000003/ScoringFiles/PGS000003.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
PPM000106 PGS000045
(BCPRS_Overall)
 PSS000070|
European Ancestry|
15,252 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
8,211 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
15,252 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
8,211 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
15,252 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
8,211 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
15,252 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
8,211 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
15,252 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
15,252 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
15,252 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
8,211 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
8,211 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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|
European Ancestry|
8,211 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (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) 		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