Polygenic Score (PGS) ID: PGS000346

Predicted Trait
Reported Trait Estrogen receptor negative breast cancer
Mapped Trait(s) estrogen-receptor negative breast cancer (EFO_1000650)
Released in PGS Catalog: Dec. 8, 2020
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Terms and Licenses
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Score Details

Score Construction
PGS Name PRS287_ERneg
Variants
Original Genome Build GRCh37
Number of Variants 287
Development Method
Name 313 variants from Mavaddatt et al (PGS000006)
Parameters p < 10e5, Imputation accuracy > 0.9 in MyBrCa and SGBCC studies
PGS Source
PGS Catalog Publication (PGP) ID PGP000112
Citation (link to publication) Ho WK et al. Nat Commun (2020)

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
[
  • 94,075 cases
  • , 75,017 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
Scores were developed in PGP000002 (Mavaddat et al. AJHG [2020]) - numbers correspond to the training + validation sets for breast cancer

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
PPM000975 PSS000493 PGP000112
Ho WK et al. (2020)
Reported Trait: ER-negative breast cancer OR: 1.41 [1.36, 1.46] AUROC: 0.594 PCs (1-10), study, array,batch Standardised to SDs of PRs in European controls
PPM000978 PSS000495 PGP000112
Ho WK et al. (2020)
Reported Trait: ER-negative breast cancer OR: 1.43 [1.35, 1.52] PCs (1-10), study, array,batch
PPM000981 PSS000498 PGP000112
Ho WK et al. (2020)
Reported Trait: ER-negative breast cancer OR: 1.49 [1.26, 1.75] AUROC: 0.587 PCs (1-10), study, array,batch Standardised to SDs of PRs in European controls

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
PSS000493
[
  • 4,764 cases
  • , 16,483 controls
]
,
0.0 % Male samples
Asian unspecified 10 cohorts
  • ACP
  • ,HERPACC
  • ,HKBCS
  • ,KOHBRA
  • ,MyBrCA
  • ,NagBCS
  • ,SBCGS
  • ,SEBCS
  • ,SGBCC
  • ,TWBCS
PSS000495
[
  • 1,365 cases
  • , 5,156 controls
]
,
0.0 % Male samples
East Asian
(Chinese)
MyBrCa, SGBCC
PSS000495
[
  • 336 cases
  • , 1,332 controls
]
,
0.0 % Male samples
South East Asian
(Malay)
MyBrCa, SGBCC
PSS000495
[
  • 184 cases
  • , 1,018 controls
]
,
0.0 % Male samples
South Asian
(Indian)
MyBrCa, SGBCC
PSS000498
[
  • 280 cases
  • , 1,212 controls
]
Asian unspecified CanBCS, LAABC, NC-BCFR