Polygenic Score (PGS) ID: PGS004867

Predicted Trait
Reported Trait ER-negative breast cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS Catalog: April 18, 2024
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Score Details

Score Construction
PGS Name PRS105_ERnegBC
Development Method
Name Genome-wide significant SNPs
Parameters effect estimates from a GWAS of ER-positive BC were used to weight an SNP if the P value from a case-only heterogeneity test (ER-positive v ER-negative disease) was < .05 and overall BC effect estimates were used as weights otherwise
Variants
Original Genome Build GRCh37
Number of Variants 105
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000612
Citation (link to publication) Gao C et al. J Clin Oncol (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 96.9%
East Asian: 1.7%
African: 1.2%
Not Reported: 0.2%
308,466 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003845
Europe PMC: 27117709
 19,291 individuals European NR
GWAS Catalog: GCST003842
Europe PMC: 27117709
 19,291 individuals European NR
GWAS Catalog: GCST001930
Europe PMC: 23535733
 39,387 individuals European NR
GWAS Catalog: GCST007302
Europe PMC: 23544012
 8,211 individuals European NR
GWAS Catalog: GCST000846
Europe PMC: 21060860
 1,703 individuals European NR
GWAS Catalog: GCST000162
Europe PMC: 18326623
 548 individuals European NR
GWAS Catalog: GCST002667
Europe PMC: 25342443
 7,600 individuals European NR
GWAS Catalog: GCST001420
Europe PMC: 22383897
 5,242 individuals East Asian NR
Europe PMC: 25855707
[
  • 5,738 cases
  • , 32,984 controls
]
,
0.0 % Male samples
 European BCAC
GWAS Catalog: GCST004950
Europe PMC: 25751625
 33,864 individuals European NR
Europe PMC: 24943594
[
  • 46,450 cases
  • , 42,600 controls
]
,
0.0 % Male samples
 European BCAC
GWAS Catalog: GCST000079
Europe PMC: 17903305
 723 individuals Not reported NR
GWAS Catalog: GCST001683
Europe PMC: 22976474
 32,530 individuals European NR
GWAS Catalog: GCST001683
Europe PMC: 22976474
 3,748 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST000678
Europe PMC: 20453838
 8,556 individuals European NR

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) 		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
PPM021106 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 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 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 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 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 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 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

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
 —