Polygenic Score (PGS) ID: PGS000003

Predicted Trait
Reported Trait ER-negative breast cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name PRS77_ERneg
Development Method
Name SNPs passing genome-wide significance
Parameters P<5x10-8
Variants
Original Genome Build NR
Number of Variants 77
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000001
Citation (link to publication) Mavaddat N et al. J Natl Cancer Inst (2015)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
22,627 individuals (100%)
PGS Evaluation
European: 100%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001937
Europe PMC: 23535729
 22,627 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
PPM000013 PSS000006|
European Ancestry|
11,428 individuals
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
|Ext.		 Reported Trait: ER-negative breast cancer OR: 1.35 [1.27, 1.43] AUROC: 0.584 — study, genetic PCs 1-15 —
PPM000116 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 —
PPM000119 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 —
PPM000003 PSS000002|
European Ancestry|
38,722 individuals
 PGP000001 |
Mavaddat N et al. J Natl Cancer Inst (2015)
 Reported Trait: ER-negative breast cancer OR: 1.45 [1.4, 1.49] — — — —

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
PSS000006 ER-negative breast cancer cases —
[
  • 1,259 cases
  • , 10,169 controls
]
,
0.0 % Male samples
 — European — 10 cohorts
  • AHS
  • ,BGS
  • ,EPIC
  • ,FHRISK
  • ,KARMA
  • ,NHS
  • ,NHS2
  • ,PLCO
  • ,PROCAS
  • ,SISTER
 Prospective Test Set
PSS000002 ER-negative breast cancer —
[
  • 5,738 cases
  • , 32,984 controls
]
 — European — 33 cohorts
  • ABCFS
  • ,ABCS
  • ,BBCC
  • ,BIGGS
  • ,BSUCH
  • ,CECILE
  • ,CGPS
  • ,CTS
  • ,DEMOKRITOS
  • ,ESTHER
  • ,GENICA
  • ,HMBCS
  • ,KBCP
  • ,LMBC
  • ,MARIE
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MTLGEBCS
  • ,NBHS
  • ,NorBCS
  • ,OBCS
  • ,ORIGO
  • ,OSU
  • ,PBCS
  • ,RPCI
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UKBGS
  • ,pKARMA
 iCOGS
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