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.Show more
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

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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 cancerbreast carcinoma88
G
-
E
https://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 cancerestrogen-receptor positive breast cancer87
G
-
E
https://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 cancerestrogen-receptor negative breast cancer53
G
-
E
https://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 cancerovarian carcinoma17
G
-
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000048/ScoringFiles/PGS000048.txt.gz
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External PGS Evaluated By This Publication

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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 cancerbreast carcinoma77
G
-
E
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 cancerestrogen-receptor positive breast cancer77
G
-
E
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 cancerestrogen-receptor negative breast cancer77
G
-
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000003/ScoringFiles/PGS000003.txt.gz
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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.

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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
PPM000106PGS000045
(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 carriersHR: 1.14 [1.11, 1.17]C-index: 0.541 [0.53, 0.551]Country, birth year
PPM000107PGS000045
(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 carriersHR: 1.22 [1.17, 1.28]C-index: 0.566 [0.551, 0.581]Country, birth year
PPM000108PGS000046
(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 carriersHR: 1.11 [1.08, 1.15]C-index: 0.532 [0.522, 0.543]Country, birth year
PPM000109PGS000046
(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 carriersHR: 1.22 [1.16, 1.27]C-index: 0.566 [0.551, 0.581]Country, birth year
PPM000110PGS000047
(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 carriersHR: 1.27 [1.23, 1.31]C-index: 0.581 [0.571, 0.592]Country, birth year
PPM000111PGS000047
(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 carriersHR: 1.15 [1.1, 1.2]C-index: 0.538 [0.523, 0.553]Country, birth year
PPM000112PGS000048
(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 carriersHR: 1.28 [1.22, 1.34]C-index: 0.579 [0.559, 0.6]Country, birth year
PPM000113PGS000048
(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 carriersHR: 1.49 [1.34, 1.65]C-index: 0.628 [0.592, 0.665]Country, birth year
PPM000114PGS000001
(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 carriersHR: 1.13 [1.1, 1.16]Country, birth year
PPM000115PGS000002
(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 carriersHR: 1.09 [1.06, 1.12]Country, birth year
PPM000116PGS000003
(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 carriersHR: 1.24 [1.21, 1.28]Country, birth year
PPM000117PGS000001
(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 carriersHR: 1.22 [1.17, 1.28]Country, birth year
PPM000118PGS000002
(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 carriersHR: 1.22 [1.17, 1.27]Country, birth year
PPM000119PGS000003
(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 carriersHR: 1.13 [1.08, 1.18]Country, birth year
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Evaluated Samples

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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
PSS000070BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylact... ic mastectomy, or age at last observation whichever occurred first.Show more
[
  • 7,797 cases
  • , 7,455 controls
]
,
0.0 % Male samples
EuropeanSome analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestryCIMBAMedian censoring age (cases) = 40
PSS000071BRCA2 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylact... ic mastectomy, or age at last observation whichever occurred first.Show more
[
  • 4,330 cases
  • , 3,881 controls
]
,
0.0 % Male samples
EuropeanSome analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestryCIMBAMedian censoring age (cases) = 43
PSS000072BRCA1 mutation carriers were followed until the age of ovarian cancer diagnosis, age at risk-reducin... g salpingo-oophorectomy (RRSO) or age at last observation. Breast cancer diagnosis was not considered as a censoring event in the ovarian cancer analysisShow more
[
  • 2,462 cases
  • , 12,790 controls
]
,
0.0 % Male samples
EuropeanSome analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestryCIMBAMedian censoring age (cases) = 50
PSS000073BRCA2 mutation carriers were followed until the age of ovarian cancer diagnosis, age at risk-reducin... g salpingo-oophorectomy (RRSO) or age at last observation. Breast cancer diagnosis was not considered as a censoring event in the ovarian cancer analysisShow more
[
  • 631 cases
  • , 7,580 controls
]
,
0.0 % Male samples
EuropeanSome analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestryCIMBAMedian censoring age (cases) = 57
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