Polygenic Score (PGS) ID: PGS000775

Predicted Trait
Reported Trait Estrogen receptor negative breast cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS Catalog: May 28, 2021
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Score Details

Score Construction
PGS Name PRS179_ERneg
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 179
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000179
Citation (link to publication) Du Z et al. J Natl Cancer Inst (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
227,101 individuals (100%)
PGS Evaluation
Multi-ancestry (excluding European): 100%
  • African
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST005077
Europe PMC: 29058716
 87,827 individuals European 127 cohorts
  • 2SISTER
  • ,ABCFS
  • ,ABCS
  • ,ABCTB
  • ,AOCS
  • ,BBCC
  • ,BBCS
  • ,BCEES
  • ,BCFR
  • ,BCFR-AU
  • ,BCFR-NY
  • ,BCFR-ONT
  • ,BCFR-PA
  • ,BCFR-UT
  • ,BCINIS
  • ,BFBOCC
  • ,BIDMC
  • ,BIGGS
  • ,BMBSA
  • ,BPC3
  • ,BREOGAN
  • ,BRICOH
  • ,BSUCH
  • ,CBCS
  • ,CCGP
  • ,CECILE
  • ,CGPS
  • ,CNIO
  • ,CNIO-BCS
  • ,COH
  • ,CONSIT_TEAM
  • ,CPSII
  • ,CTS
  • ,DEMOKRITOS
  • ,DFCI
  • ,DIETCOMPLYF
  • ,DKFZ
  • ,EMBRACE
  • ,EPIC
  • ,ESTHER
  • ,FCCC
  • ,FPGMX
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,GENICA
  • ,GEPARSIXTO
  • ,GESBC
  • ,GWAS_UK2
  • ,Georgetown
  • ,HABCS
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HMBCS
  • ,HUBCS
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,IHCC
  • ,INHERIT
  • ,IOVHBOCS
  • ,IPOBCS
  • ,KARBAC
  • ,KBCP
  • ,KUMC
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MAYO
  • ,MBCSG
  • ,MCCS
  • ,MCGILL
  • ,MDACCS
  • ,MEC
  • ,MISS
  • ,MMHS
  • ,MODSQUAD
  • ,MSKCC
  • ,MTLGEBCS
  • ,MUV
  • ,NAROD
  • ,NBCS
  • ,NBHS
  • ,NC-BCFR
  • ,NCI
  • ,NHS
  • ,NHS2
  • ,NNPIO
  • ,NRG_ONCOLOGY
  • ,NSUHS
  • ,OBCS
  • ,OCGN
  • ,OFBCR
  • ,ORIGO
  • ,OSU
  • ,OSUCCG
  • ,OUH
  • ,PBCS
  • ,PLCO
  • ,POSH
  • ,PREFACE
  • ,RBCS
  • ,RPCI
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SISTER
  • ,SKKDKFZS
  • ,SMC
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SWE-BRCA
  • ,SZBCS
  • ,TNBCC
  • ,UC
  • ,UCIBCS
  • ,UCSF
  • ,UKBGS
  • ,UKGRFOCR
  • ,UKOPS
  • ,UPENN
  • ,UPITT
  • ,VFCTG
  • ,WCRI
  • ,kConFab
  • ,pKARMA
GWAS Catalog: GCST004988
Europe PMC: 29059683
 139,274 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
PPM002009 PSS000995|
Multi-ancestry (excluding European)|
19,434 individuals
 PGP000179 |
Du Z et al. J Natl Cancer Inst (2021)
 Reported Trait: Estrogen-receptor negative breast cancer OR: 1.31 [1.24, 1.37] — — Age, study, PCs(1-10) Only 163 of the original 179 SNPs were avaialble in all consortia (imputation score r^2 < 0.8).For missing variants (not genotyped or imputed) in one study, each individual in that study was assigned the expected dosage derived from the remainder of studies
PPM002010 PSS000995|
Multi-ancestry (excluding European)|
19,434 individuals
 PGP000179 |
Du Z et al. J Natl Cancer Inst (2021)
 Reported Trait: Estrogen-receptor negative breast cancer — AUROC: 0.578 [0.564, 0.591] — Study, PCs(1-10) Only 163 of the original 179 SNPs were avaialble in all consortia (imputation score r^2 < 0.8).For missing variants (not genotyped or imputed) in one study, each individual in that study was assigned the expected dosage derived from the remainder of studies

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
PSS000995 Cases are women with breast cancer. Of the 3928 breast cancer cases, 1533 were ER-positive and 987 were ER-negative. —
[
  • 3,928 cases
  • , 3,435 controls
]
,
0.0 % Male samples
 Mean = 47.71 years African American or Afro-Caribbean, Sub-Saharan African, African unspecified — 15 cohorts
  • 2SISTER
  • ,BBCS
  • ,BNCS
  • ,CCPS
  • ,MEC
  • ,NBHS
  • ,NC-BCFR
  • ,NCBCS
  • ,NigBCS
  • ,PLCO
  • ,RVGBC
  • ,SCCS
  • ,SISTER
  • ,USRT
  • ,WAABCS
 All cohorts part of The GAME-ON OncoArray Consortium or The GWAS of Breast Cancer in the African Diaspora Consortium (ROOT)
PSS000995 Cases are women with breast cancer. Of the 899 breast cancer cases, 296 were ER-positive and 277 were ER-negative. —
[
  • 899 cases
  • , 1,630 controls
]
,
0.0 % Male samples
 — Sub-Saharan African — GBHS —
PSS000995 Cases are women with breast cancer. Of the 4414 breast cancer cases, 2470 were ER-positive and 1372 were ER-negative. —
[
  • 4,414 cases
  • , 5,128 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean — 10 cohorts
  • BWHS
  • ,CARE
  • ,CBCS
  • ,MEC
  • ,NBHS
  • ,NC-BCFR
  • ,PLCO
  • ,SFBCS
  • ,WCHS
  • ,WFBC
 All cohorts part of African American Breast Cancer (AABC) consortium and/or The African American Breast Cancer Epidemiology and Risk (AMBER)consortium.