Polygenic Score (PGS) ID: PGS000004

Predicted Trait
Reported Trait Breast Cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS: Oct. 14, 2019

Score Details

Score Construction
PGS Name PRS313_BC
Variants
Original Genome Build GRCh37
Number of Variants 313
Development Method
Name Hard-Thresholding Stepwise Forward Regression
Parameters p < 10^-5
PGS Source
PGS Catalog Publication (PGP) ID PGP000002
Citation (link to publication) Mavaddat N et al. Am J Hum Genet (2018)

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
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
Invasive breast cancer-affected
[
  • 88,916 cases
  • , 69,732 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
Training Cohort
Invasive breast cancer-affected
[
  • 5,159 cases
  • , 5,285 controls
]
,
0.0 % Male samples
European 25 cohorts
  • ABCTB
  • ,BBCC
  • ,BCEES
  • ,BCINIS
  • ,BREOGAN
  • ,CBCS
  • ,CCGP
  • ,CGPS
  • ,CPSII
  • ,CTS
  • ,GENICA
  • ,HMBCS
  • ,LMBC
  • ,MCBCS
  • ,MCCS
  • ,MISS
  • ,MMHS
  • ,NBHS
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,SEARCH
  • ,SMC
  • ,UCIBCS
  • ,WHI
Validation Cohort

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
PPM000005 PSS000007 PGP000002
Mavaddat N et al. (2018)
Reported Trait: Incident breast cancer cases HR: 1.59[1.54, 1.64] study, genetic PCs 1-15 Included only 306 of the 313 SNPs
PPM000004 PSS000004 PGP000002
Mavaddat N et al. (2018)
Reported Trait: Invasive breast cancer OR: 1.61[1.57, 1.65] AUROC: 0.63 study, genetic PCs 1-15

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000004 Invasive breast cancer-affected
[
  • 11,428 cases
  • , 18,323 controls
]
,
0.0 % Male samples
European 10 cohorts
  • AHS
  • ,BGS
  • ,EPIC
  • ,FHRISK
  • ,KARMA
  • ,NHS
  • ,NHS2
  • ,PLCO
  • ,PROCAS
  • ,SISTER
Prospective Test Set
PSS000007 Incident registry-confirmed invasive breast cancers developed
[
  • 3,215 cases
  • , 186,825 controls
]
,
0.0 % Male samples
European UKB Prospective Test Set (UKB)