Polygenic Score (PGS) ID: PGS000008

Predicted Trait
Reported Trait ER-positive Breast Cancer
Mapped Trait(s) estrogen-receptor positive breast cancer (EFO_1000649)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name PRS3820_ERpos
Variants
Original Genome Build GRCh37
Number of Variants 3,820
Development Method
Name LASSO penalized regression
Parameters p < 0.001
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
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
ER-positive breast cancer cases —
[
  • 55,391 cases
  • , 31,977 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
  • ,POSH
  • ,PREFACE
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SMC
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SZBCS
  • ,TNBCC
  • ,UCIBCS
  • ,UKOPS
  • ,WHI
  • ,pKARMA
 Training Cohort
ER-positive breast cancer cases —
[
  • 4,233 cases
  • , 926 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
  • ,SEARCH
  • ,SMC
  • ,UCIBCS
  • ,WHI
  • ,pKARMA
 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
PPM000009 PSS000005 PGP000002 Mavaddat N et al. (2018) Reported Trait: ER-positive breast cancer OR: 1.73 [1.68, 1.78] AUROC: 0.647 — study, genetic PCs 1-15 —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
PSS000005 ER-positive breast cancer cases —
[
  • 7,992 cases
  • , 3,436 controls
]
,
0.0 % Male samples
 — European — 10 cohorts
  • AHS
  • ,BGS
  • ,EPIC
  • ,FHRISK
  • ,KARMA
  • ,NHS
  • ,NHS2
  • ,PLCO
  • ,PROCAS
  • ,SISTER
 Prospective Test Set