Polygenic Score (PGS) ID: PGS000347

Predicted Trait
Reported Trait Estrogen receptor positive breast cancer
Mapped Trait(s) estrogen-receptor positive breast cancer (EFO_1000649)
Released in PGS Catalog: Dec. 8, 2020
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Terms and Licenses
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_ERpos
Variants
Original Genome Build GRCh37
Number of Variants 287
Development Method
Name 313 variants from Mavaddatt et al (PGS000005)
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)
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
GWAS Catalog: GCST004988
Europe PMC: 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
  • ,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
PPM000980 PSS000499|
Additional Asian Ancestries|
2,234 individuals
PGP000112 |
Ho WK et al. Nat Commun (2020)
Reported Trait: ER-positive breast cancer OR: 1.38 [1.25, 1.53] AUROC: 0.586 PCs (1-10), study, array,batch Standardised to SDs of PRs in European controls
PPM000977 PSS000496|
Multi-ancestry (excluding European)|
12,222 individuals
PGP000112 |
Ho WK et al. Nat Commun (2020)
Reported Trait: ER-positive breast cancer OR: 1.59 [1.53, 1.66] PCs (1-10), study, array,batch
PPM000974 PSS000492|
Additional Asian Ancestries|
26,960 individuals
PGP000112 |
Ho WK et al. Nat Commun (2020)
Reported Trait: ER-positive breast cancer OR: 1.62 [1.57, 1.67] AUROC: 0.627 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
PSS000492
[
  • 10,477 cases
  • , 16,483 controls
]
,
0.0 % Male samples
Asian unspecified 10 cohorts
  • ACP
  • ,HERPACC
  • ,HKBCS
  • ,KOHBRA
  • ,MYBRCA
  • ,NagBCS
  • ,SBCGS
  • ,SEBCS
  • ,SGBCC
  • ,TWBCS
PSS000496
[
  • 3,627 cases
  • , 5,156 controls
]
,
0.0 % Male samples
East Asian
(Chinese)
MYBRCA, SGBCC
PSS000496
[
  • 715 cases
  • , 1,332 controls
]
,
0.0 % Male samples
South East Asian
(Malay)
MYBRCA, SGBCC
PSS000496
[
  • 374 cases
  • , 1,018 controls
]
,
0.0 % Male samples
South Asian
(Indian)
MYBRCA, SGBCC
PSS000499
[
  • 1,022 cases
  • , 1,212 controls
]
Asian unspecified CanBCS, LAABC, NC-BCFR