Polygenic Score (PGS) ID: PGS000345

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
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 PRS229_BC
Development Method
Name 313 variants from Mavaddatt et al (PGS000004)
Parameters p < 10e5, Imputation accuracy >0.9 in MyBrCa and SGBCC studies, polymorphic variants
Variants
Original Genome Build GRCh37
Number of Variants 229
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%
East Asian: 33.3%
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
PPM000983 PSS000491|
Additional Asian Ancestries|
32,238 individuals
 PGP000112 |
Ho WK et al. Nat Commun (2020)
 Reported Trait: Breast cancer OR: 1.49 [1.45, 1.52] AUROC: 0.611 — PCs (1-10), study, array,batch Standardised to SDs of PRs in European controls
PPM000982 PSS000500|
East Asian Ancestry|
10,255 individuals
 PGP000112 |
Ho WK et al. Nat Commun (2020)
 Reported Trait: Incident breast cancer HR: 1.49 [1.33, 1.67] C-index: 0.61 — PCs (1-7), study, array,batch Standardised to SDs of PRs in European controls
PPM000984 PSS000497|
Additional Asian Ancestries|
2,719 individuals
 PGP000112 |
Ho WK et al. Nat Commun (2020)
 Reported Trait: Breast cancer OR: 1.33 [1.22, 1.45] AUROC: 0.579 — 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
PSS000500 — —
[
  • 413 cases
  • , 9,842 controls
]
,
0.0 % Male samples
 — East Asian
(Chinese)		 — SCHS —
PSS000491 — —
[
  • 15,755 cases
  • , 16,483 controls
]
,
0.0 % Male samples
 — Asian unspecified — 10 cohorts
  • ACP
  • ,HERPACC
  • ,HKBCS
  • ,KOHBRA
  • ,MYBRCA
  • ,NagBCS
  • ,SBCGS
  • ,SEBCS
  • ,SGBCC
  • ,TWBCS
 —
PSS000497 — —
[
  • 1,507 cases
  • , 1,212 controls
]
,
0.0 % Male samples
 — Asian unspecified — CanBCS, LAABC, NC-BCFR —