Polygenic Score (PGS) ID: PGS000001

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

Score Construction
PGS Name PRS77_BC
Variants
Original Genome Build NR
Number of Variants 77
Development Method
Name SNPs passing genome-wide significance
Parameters P<5x10-8
PGS Source
PGS Catalog Publication (PGP) ID PGP000001
Citation (link to publication) Mavaddat N et al. J Natl Cancer Inst (2015)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001937
EuropePMC: 23535729		 22,627 individuals European

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
PPM000011 PSS000004 PGP000002
Mavaddat N et al. Am J Hum Genet (2018)
Ext.		 Reported Trait: Invasive breast cancer OR: 1.46 [1.42, 1.49] AUROC: 0.603 — study, genetic PCs 1-15 —
PPM000114 PSS000070 PGP000033
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
Ext.		 Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.13 [1.1, 1.16] — — Country, birth year —
PPM000117 PSS000071 PGP000033
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
Ext.		 Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22 [1.17, 1.28] — — Country, birth year —
PPM000001 PSS000001 PGP000001
Mavaddat N et al. J Natl Cancer Inst (2015)
 Reported Trait: All breast cancer OR: 1.55 [1.52, 1.58] C-index: 0.622 [0.619, 0.627] — — —
PPM000962 PSS000486 PGP000109
Kramer I et al. Am J Hum Genet (2020)
Ext.		 Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.21 [1.13, 1.29] — — Country —
PPM000961 PSS000484 PGP000109
Kramer I et al. Am J Hum Genet (2020)
Ext.		 Reported Trait: Metachronous contralateral breast cancer HR: 1.21 [1.14, 1.29] — — Country —
PPM000945 PSS000486 PGP000109
Kramer I et al. Am J Hum Genet (2020)
Ext.		 Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.21 [1.13, 1.29] — — Country —
PPM000944 PSS000484 PGP000109
Kramer I et al. Am J Hum Genet (2020)
Ext.		 Reported Trait: Metachronous contralateral breast cancer HR: 1.21 [1.14, 1.29] — — Country —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
PSS000001 All breast cancer —
[
  • 33,673 cases
  • , 33,381 controls
]
 — European — 33 cohorts
  • ABCFS
  • ,ABCS
  • ,BBCC
  • ,BIGGS
  • ,BSUCH
  • ,CECILE
  • ,CGPS
  • ,CTS
  • ,DEMOKRITOS
  • ,ESTHER
  • ,GENICA
  • ,HMBCS
  • ,KBCP
  • ,LMBC
  • ,MARIE
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MTLGEBCS
  • ,NBHS
  • ,NorBCS
  • ,OBCS
  • ,ORIGO
  • ,OSU
  • ,PBCS
  • ,RPCI
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UKBGS
  • ,pKARMA
 iCOGS
PSS000484 Women (European Ancestry) diagnosed with unilateral breast cancer or metachronous contralateral breast cancer (CBC). Metachronous contralateral breast cancer was defined as breast cancer in the contralateral breast (in situ or invasive) diagnosed at least 3 months after the first breast cancer. Median = 8.4 years
[
  • 1,027 cases
  • , 55,041 controls
]
,
0.0 % Male samples
 Median (Age At Diagnosis) = 56.0 years European — 42 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,AOCS
  • ,BBCC
  • ,BCFR-PA
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CCGP
  • ,CGPS
  • ,GC-HBOC
  • ,GENICA
  • ,HCSC
  • ,HEBCS
  • ,KARBAC
  • ,KARMA
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MEC
  • ,MISS
  • ,NBCS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,POSH
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UCIBCS
  • ,kConFab
  • ,pKARMA
 —
PSS000486 Women (European Ancestry) diagnosed with unilateral breast cancer or metachronous contralateral breast cancer (CBC). Metachronous contralateral breast cancer was defined as breast cancer in the contralateral breast (in situ or invasive) diagnosed at least 3 months after the first breast cancer. Median = 8.4 years
[
  • 923 cases
  • , 55,145 controls
]
,
0.0 % Male samples
 Median (Age At Diagnosis) = 56.0 years European — 42 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,AOCS
  • ,BBCC
  • ,BCFR-PA
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CCGP
  • ,CGPS
  • ,GC-HBOC
  • ,GENICA
  • ,HCSC
  • ,HEBCS
  • ,KARBAC
  • ,KARMA
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MEC
  • ,MISS
  • ,NBCS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,POSH
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UCIBCS
  • ,kConFab
  • ,pKARMA
 —
PSS000070 BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. —
[
  • 7,797 cases
  • , 7,455 controls
]
,
0.0 % Male samples
 — European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 40
PSS000071 BRCA2 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. —
[
  • 4,330 cases
  • , 3,881 controls
]
,
0.0 % Male samples
 — European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 43
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