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 |
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 |
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 |
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 |
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 |
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 |
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 | — |
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
|
---|---|---|---|---|---|---|---|---|
PSS000070 | BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylact... ic mastectomy, or age at last observation whichever occurred first.Show more | — | [ ,
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 prophylact... ic mastectomy, or age at last observation whichever occurred first.Show more | — | [ ,
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 |
PSS000072 | BRCA1 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 | — | [ ,
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-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 | — | [ ,
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 |