Polygenic Score (PGS) ID: PGS000007

Predicted Trait
Reported Trait Breast Cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
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Score Details

Score Construction
PGS Name PRS3820_BC
Variants
Original Genome Build GRCh37
Number of Variants 3,820
Development Method
Name LASSO penalized regression
Parameters p < 0.001
PGS Source
PGS Catalog Publication (PGP) ID PGP000002
Citation (link to publication) Mavaddat N et al. Am J Hum Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
Score Development/Training
European: 100%
169,092 individuals (100%)
PGS Evaluation
European: 100%
2 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
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
  • ,SEARCH
  • ,SMC
  • ,UCIBCS
  • ,WHI
  • ,pKARMA
Validation Cohort
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
  • ,POSH
  • ,PREFACE
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SMC
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SZBCS
  • ,TNBCC
  • ,UCIBCS
  • ,UKOPS
  • ,WHI
  • ,pKARMA
Training 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)
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
PPM000008 PSS000004|
European Ancestry|
29,751 individuals
PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
Reported Trait: Invasive breast cancer OR: 1.66 [1.61, 1.7] AUROC: 0.636 study, genetic PCs 1-15
PPM000388 PSS000218|
European Ancestry|
9,529 individuals
PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.
Reported Trait: Breast Cancer (personal history) AUROC: 0.63
PPM000384 PSS000218|
European Ancestry|
9,529 individuals
PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.
Reported Trait: Breast Cancer (personal history) OR: 1.56 [1.45, 1.68] age at menarche
PPM000386 PSS000218|
European Ancestry|
9,529 individuals
PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.
Reported Trait: Breast Cancer (personal history) AUROC: 0.78 age, sex

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
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
PSS000218 Phenotypic information was self-reported by the individual through an online, interactive health history tool
[
  • 828 cases
  • , 8,701 controls
]
,
0.0 % Male samples
European CG Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test