PGS Publication: PGP000612

Publication Information (EuropePMC)
Title Risk of Breast Cancer Among Carriers of Pathogenic Variants in Breast Cancer Predisposition Genes Varies by Polygenic Risk Score.
PubMed ID 34101481(Europe PMC)
doi 10.1200/jco.20.01992
Publication Date June 8, 2021
Journal J Clin Oncol
Author(s) Gao C, Polley EC, Hart SN, Huang H, Hu C, Gnanaolivu R, Lilyquist J, Boddicker NJ, Na J, Ambrosone CB, Auer PL, Bernstein L, Burnside ES, Eliassen AH, Gaudet MM, Haiman C, Hunter DJ, Jacobs EJ, John EM, Lindström S, Ma H, Neuhausen SL, Newcomb PA, O'Brien KM, Olson JE, Ong IM, Patel AV, Palmer JR, Sandler DP, Tamimi R, Taylor JA, Teras LR, Trentham-Dietz A, Vachon CM, Weinberg CR, Yao S, Weitzel JN, Goldgar DE, Domchek SM, Nathanson KL, Couch FJ, Kraft P.
Released in PGS Catalog: April 18, 2024

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)
PGS004865
(PRS105_BC)
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Breast cancer breast carcinoma 105
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004865/ScoringFiles/PGS004865.txt.gz
PGS004866
(PRS105_ERposBC)
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 ER-positive breast cancer estrogen-receptor positive breast cancer 105
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004866/ScoringFiles/PGS004866.txt.gz
PGS004867
(PRS105_ERnegBC)
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 ER-negative breast cancer estrogen-receptor negative breast cancer 105
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004867/ScoringFiles/PGS004867.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
PPM021102 PGS004865
(PRS105_BC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BRAC2 carriers younger than 40 years OR: 18.2 [9.36, 35.4] — — — Odds ratio is for a 1-SD change from the median PRS in BRCA2 variant carriers vs non-carriers
PPM021103 PGS004865
(PRS105_BC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among ATM carriers younger than 40 years OR: 3.19 [2.51, 4.05] — — — Odds ratio is for a 1-SD change from the median PRS in ATM variant carriers vs non-carriers
PPM021104 PGS004865
(PRS105_BC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among CHEK2 carriers younger than 40 years OR: 3.84 [3.12, 4.72] — — — Odds ratio is for a 1-SD change from the median PRS in CHEK2 variant carriers vs non-carriers
PPM021105 PGS004865
(PRS105_BC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among PALB2 carriers younger than 40 years OR: 5.67 [3.84, 8.38] — — — Odds ratio is for a 1-SD change from the median PRS in PALB2 variant carriers vs non-carriers
PPM021106 PGS004867
(PRS105_ERnegBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BRAC1 carriers younger than 40 years OR: 61.05 [25.31, 147.28] — — — Odds ratio is for a 1-SD change from the median PRS in BRCA1 variant carriers vs non-carriers
PPM021107 PGS004867
(PRS105_ERnegBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BRAC2 carriers younger than 40 years OR: 13.16 [4.29, 35.2] — — — Odds ratio is for a 1-SD change from the median PRS in BRCA2 variant carriers vs non-carriers
PPM021108 PGS004867
(PRS105_ERnegBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among ATM carriers younger than 40 years OR: 1.78 [0.92, 3.46] — — — Odds ratio is for a 1-SD change from the median PRS in ATM variant carriers vs non-carriers
PPM021109 PGS004867
(PRS105_ERnegBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among CHEK2 carriers younger than 40 years OR: 1.79 [1.02, 3.14] — — — Odds ratio is for a 1-SD change from the median PRS in CHEK2 variant carriers vs non-carriers
PPM021110 PGS004867
(PRS105_ERnegBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among PALB2 carriers younger than 40 years OR: 11.95 [6.41, 22.3] — — — Odds ratio is for a 1-SD change from the median PRS in PALB2 variant carriers vs non-carriers
PPM021111 PGS004867
(PRS105_ERnegBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BARD1 carriers younger than 40 years OR: 4.42 [1.9, 10.3] — — — Odds ratio is for a 1-SD change from the median PRS in BARD1 variant carriers vs non-carriers
PPM021112 PGS004867
(PRS105_ERnegBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BRIP1 carriers younger than 40 years OR: 2.45 [1.0, 5.97] — — — Odds ratio is for a 1-SD change from the median PRS in BRIP1 variant carriers vs non-carriers
PPM021113 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BRAC1 carriers younger than 40 years OR: 15.04 [6.06, 37.34] — — — Odds ratio is for a 1-SD change from the median PRS in BRCA1 variant carriers vs non-carriers
PPM021114 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BRAC2 carriers younger than 40 years OR: 21.24 [9.84, 45.84] — — — Odds ratio is for a 1-SD change from the median PRS in BRCA2 variant carriers vs non-carriers
PPM021115 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among ATM carriers younger than 40 years OR: 4.17 [3.06, 5.68] — — — Odds ratio is for a 1-SD change from the median PRS in ATM variant carriers vs non-carriers
PPM021101 PGS004865
(PRS105_BC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BRAC1 carriers younger than 40 years OR: 16.2 [8.1, 32.5] — — — Odds ratio is for a 1-SD change from the median PRS in BRCA1 variant carriers vs non-carriers
PPM021116 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among CHEK2 carriers younger than 40 years OR: 4.86 [3.71, 6.37] — — — Odds ratio is for a 1-SD change from the median PRS in CHEK2 variant carriers vs non-carriers
PPM021117 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among PALB2 carriers younger than 40 years OR: 6.51 [4.0, 10.6] — — — Odds ratio is for a 1-SD change from the median PRS in PALB2 variant carriers vs non-carriers
PPM021118 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BARD1 carriers younger than 40 years OR: 1.94 [1.02, 3.68] — — — Odds ratio is for a 1-SD change from the median PRS in BARD1 variant carriers vs non-carriers
PPM021119 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among BRIP1 carriers younger than 40 years OR: 2.73 [1.65, 4.54] — — — Odds ratio is for a 1-SD change from the median PRS in BRIP1 variant carriers vs non-carriers
PPM021120 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among CDH1 carriers younger than 40 years OR: 17.98 [3.8, 85.06] — — — Odds ratio is for a 1-SD change from the median PRS in CDH1 variant carriers vs non-carriers
PPM021121 PGS004866
(PRS105_ERposBC)
 PSS011529|
European Ancestry|
52,925 individuals
 PGP000612 |
Gao C et al. J Clin Oncol (2021)
 Reported Trait: Breast cancer among NF1 carriers younger than 40 years OR: 2.34 [0.75, 7.31] — — — Odds ratio is for a 1-SD change from the median PRS in NF1 variant carriers vs non-carriers

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
PSS011529 — —
[
  • 26,798 cases
  • , 26,127 controls
]
,
0.0 % Male samples
 — European — 11 cohorts
  • CPS
  • ,CPSII
  • ,CTS
  • ,MCBCS
  • ,MEC
  • ,MMHS
  • ,NHS
  • ,SISTER
  • ,WCHS
  • ,WHI
  • ,WWHS
 —