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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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRS287_ERneg
Development Method
Name 313 variants from Mavaddatt et al (PGS000006)
Parameters p < 10e5, Imputation accuracy > 0.9 in MyBrCa and SGBCC studies
Variants
Original Genome Build GRCh37
Number of Variants 287
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000112
Citation (link to publication) Ho WK et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
Score Development/Training
European: 100%
169,092 individuals (100%)
PGS Evaluation
Additional Asian Ancestries: 66.7%
Multi-ancestry (excluding European): 33.3%
  • East Asian
  • Additional Asian Ancestries
  • South Asian
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004988
Europe PMC: 29059683
 139,274 individuals European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 30554720
[
  • 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
  • ,POSH
  • ,PREFACE
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SMC
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SZBCS
  • ,TNBCC
  • ,UCIBCS
  • ,UKOPS
  • ,WHI
  • ,pKARMA
 — — — — 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) 		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
PPM000981 PSS000498|
Additional Asian Ancestries|
1,492 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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
PPM000978 PSS000495|
Multi-ancestry (excluding European)|
9,391 individuals
 PGP000112 |
Ho WK et al. Nat Commun (2020)
 Reported Trait: ER-negative breast cancer OR: 1.43 [1.35, 1.52] — — PCs (1-10), study, array,batch —
PPM000975 PSS000493|
Additional Asian Ancestries|
21,247 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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

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
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 —