Polygenic Score (PGS) ID: PGS001778

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Nov. 25, 2021
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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 PRS15_BC
Development Method
Name Variants significantly associated with breast cancer
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 15
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000259
Citation (link to publication) Yiangou K et al. Cancers (Basel) (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 70.9%
  • European
  • Additional Asian Ancestries
European: 26%
East Asian: 3.1%
98,087 individuals (100%)
Score Development/Training
European: 100%
112,304 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004948
Europe PMC: 19330027
754 individuals European NR
GWAS Catalog: GCST000035
Europe PMC: 17529967
754 individuals European EPIC-Norfolk
Europe PMC: 22267197
[
  • 69,564 cases
]
European, Asian unspecified 42 cohorts
  • ABCFS
  • ,ABCS
  • ,ACP
  • ,BBCC
  • ,BBCS
  • ,BIGGS
  • ,BSUCH
  • ,CECILE
  • ,CGPS
  • ,CNIO-BCS
  • ,CTS
  • ,ESTHER
  • ,GC-HBOC
  • ,GENICA
  • ,GESBC
  • ,HABCS
  • ,HEBCS
  • ,HMBCS
  • ,HUBCS
  • ,KARBAC
  • ,KBCP
  • ,KCONFAB/AOCS
  • ,LMBC
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MCCS
  • ,NBCS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SEBCS
  • ,SZBCS
  • ,SwBCS
  • ,UCIBCS
  • ,UKBGS
GWAS Catalog: GCST000037
Europe PMC: 17529974
13,145 individuals European 7 cohorts
  • ICR
  • ,IGD
  • ,KUH
  • ,MEC
  • ,ODZH
  • ,RUNMC
  • ,deCODE
GWAS Catalog: GCST000365
Europe PMC: 19330030
2,287 individuals European NHS
GWAS Catalog: GCST000678
Europe PMC: 20453838
8,556 individuals European B58C, FBCS, POSH, UKBS
GWAS Catalog: GCST000343
Europe PMC: 19219042
3,027 individuals East Asian NBHS, SBCS, SECS
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
GWAS Catalog: GCST007236
Europe PMC: 25751625
89,677 individuals European 42 cohorts
  • ABCFS
  • ,ABCS
  • ,AOCS
  • ,BBCC
  • ,BBCS
  • ,BIGGS
  • ,BSUCH
  • ,CECILE
  • ,CGPS
  • ,CNIO-BCS
  • ,CTS
  • ,DEMOKRITOS
  • ,ESTHER
  • ,GENICA
  • ,HEBCS
  • ,HMBCS
  • ,KARBAC
  • ,KBCP
  • ,LMBC
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MTLGEBCS
  • ,NBCS
  • ,NBHS
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,OSU
  • ,PBCS
  • ,RBCS
  • ,RPCI
  • ,SASBAC
  • ,SBCS_b
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UKBGS
  • ,kConFab
  • ,pKARMA
GWAS Catalog: GCST001937
Europe PMC: 23535729
22,627 individuals European 10 cohorts
  • ABCFS
  • ,BBCS
  • ,CGEMS
  • ,DFBBCS
  • ,GC-HBOC
  • ,GWAS_UK2
  • ,HEBCS
  • ,MARIE
  • ,SASBAC
  • ,kConFab

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
PPM009262 PSS007670|
European Ancestry|
1,780 individuals
PGP000259 |
Yiangou K et al. Cancers (Basel) (2021)
Reported Trait: Breast cancer OR: 1.66 [1.25, 2.2] AUROC: 0.548 Age
PPM009264 PSS007670|
European Ancestry|
1,780 individuals
PGP000259 |
Yiangou K et al. Cancers (Basel) (2021)
Reported Trait: Breast cancer OR: 1.57 [1.18, 2.08] AUROC: 0.578 Age, family history
PPM009261 PSS007670|
European Ancestry|
1,780 individuals
PGP000259 |
Yiangou K et al. Cancers (Basel) (2021)
Reported Trait: Breast cancer OR: 1.66 [1.25, 2.19] AUROC: 0.547 [0.52, 0.57]
PPM009263 PSS007670|
European Ancestry|
1,780 individuals
PGP000259 |
Yiangou K et al. Cancers (Basel) (2021)
Reported Trait: Breast cancer OR: 1.56 [1.18, 2.08] AUROC: 0.578 Family history
PPM009265 PSS007670|
European Ancestry|
1,780 individuals
PGP000259 |
Yiangou K et al. Cancers (Basel) (2021)
Reported Trait: Breast cancer AUROC: 0.6975 [0.673, 0.722] Odds Ratio (OR, top 10% vs middle10%): 4.58 [2.88, 7.4] Age at interview, menopausal status, age at menarche, age at first full-term pregnancy(1-4), parous, breast feeding, smoking status, body mass index, height, hormone-replacement therapy ever use, family history

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
PSS007670 Cases were individuals who had been diagnosed with breast cancer.
[
  • 880 cases
  • , 900 controls
]
,
0.0 % Male samples
European
(Greek-Cypriot)
NR Cases and controls were obtained from the MASTOS study.