Polygenic Score (PGS) ID: PGS000006

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

Score Details

Score Construction
PGS Name PRS313_ERneg
Variants
Original Genome Build GRCh37
Number of Variants 313
Development Method
Name Hard-Thresholding Stepwise Forward Regression
Parameters p < 10^-5
PGS Source
PGS Catalog Publication (PGP) ID PGP000002
Citation (link to publication) Mavaddat N et al. Am J Hum Genet (2018)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004988
EuropePMC: 29059683		 139,274 individuals European
Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
ER-negative breast cancer cases —
[
  • 15,404 cases
  • , 71,964 controls
]
,
0.0 % Male samples
 — European — 68 cohorts
  • 2SISTER
  • ,ABCFS
  • ,ABCS
  • ,ABCTB
  • ,AOCS
  • ,BBCC
  • ,BBCS
  • ,BCEES
  • ,BCFR-NY
  • ,BCFR-PA
  • ,BCFR-UTAH
  • ,BCINIS
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CBCS
  • ,CCGP
  • ,CECILE
  • ,CGPS
  • ,CNIO-BCS
  • ,CPSII
  • ,CTS
  • ,DIETCOMPLYF
  • ,ESTHER
  • ,GC-HBOC
  • ,GENICA
  • ,GEPARSIXTO
  • ,GESBC
  • ,HCSC
  • ,HEBCS
  • ,HMBCS
  • ,HUOCS
  • ,KARBAC
  • ,KBCP
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MISS
  • ,MMHS
  • ,MSKCC
  • ,MTLGEBCS
  • ,NBCS
  • ,NBHS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,POSH
  • ,PREFACE
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SMC
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SZBCS
  • ,TNBCC
  • ,UCIBCS
  • ,UKOPS
  • ,WHI
 Training Cohort
ER-negative breast cancer cases —
[
  • 926 cases
  • , 4,233 controls
]
,
0.0 % Male samples
 — European — 25 cohorts
  • ABCTB
  • ,BBCC
  • ,BCEES
  • ,BCINIS
  • ,BREOGAN
  • ,CBCS
  • ,CCGP
  • ,CGPS
  • ,CPSII
  • ,CTS
  • ,GENICA
  • ,HMBCS
  • ,LMBC
  • ,MCBCS
  • ,MCCS
  • ,MISS
  • ,MMHS
  • ,NBHS
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,SEARCH
  • ,SMC
  • ,UCIBCS
  • ,WHI
 Validation Cohort

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 ID) 		PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000007 PSS000006 PGP000002
Mavaddat N et al. (2018) 		Reported Trait: ER-negative breast cancer OR: 1.45[1.37, 1.53] AUROC: 0.601 — study, genetic PCs 1-15 —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		Detailed Phenotype Description 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