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
Development Method
Name SNPs passing genome-wide significance
Parameters P<5x10-8
Variants
Original Genome Build NR
Number of Variants 77
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000001
Citation (link to publication) Mavaddat N et al. J Natl Cancer Inst (2015)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
22,627 individuals (100%)
PGS Evaluation
European: 80%
Not Reported: 20%
10 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001937
Europe PMC: 23535729
 22,627 individuals European NR

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
PPM000011 PSS000004|
European Ancestry|
29,751 individuals
 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|
European Ancestry|
15,252 individuals
 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|
European Ancestry|
8,211 individuals
 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|
European Ancestry|
67,054 individuals
 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|
European Ancestry|
56,068 individuals
 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 —
PPM000945 PSS000486|
European Ancestry|
56,068 individuals
 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|
European Ancestry|
56,068 individuals
 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 —
PPM000961 PSS000484|
European Ancestry|
56,068 individuals
 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 —
PPM002152 PSS001054|
European Ancestry|
760 individuals
 PGP000198 |
Borde J et al. J Natl Cancer Inst (2020)
|Ext.		 Reported Trait: Breast cancer in CHEK2 mutation carriers 40 years of age or below HR: 1.43 [1.04, 1.97] — — Year of birth, counselling center of origin Only 70 of the original 77 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 70 SNPs used, 7 were proxies R^2>0.8.
PPM002150 PSS001054|
European Ancestry|
760 individuals
 PGP000198 |
Borde J et al. J Natl Cancer Inst (2020)
|Ext.		 Reported Trait: Breast cancer in CHEK2 mutation carriers HR: 1.71 [1.36, 2.15] — — Year of birth, counselling center of origin Only 70 of the original 77 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 70 SNPs used, 7 were proxies R^2>0.8.
PPM002151 PSS001054|
European Ancestry|
760 individuals
 PGP000198 |
Borde J et al. J Natl Cancer Inst (2020)
|Ext.		 Reported Trait: Breast cancer in CHEK2 mutation carriers HR: 2.29 [1.56, 3.38] — — Year of birth, counselling center of origin, PRS*c.1100delC carrier status Only 70 of the original 77 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 70 SNPs used, 7 were proxies R^2>0.8.
PPM002153 PSS001054|
European Ancestry|
760 individuals
 PGP000198 |
Borde J et al. J Natl Cancer Inst (2020)
|Ext.		 Reported Trait: Breast cancer in CHEK2 mutation carriers between 41 and 50 years of age HR: 2.32 [1.69, 3.2] — — Year of birth, counselling center of origin Only 70 of the original 77 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 70 SNPs used, 7 were proxies R^2>0.8.
PPM002154 PSS001054|
European Ancestry|
760 individuals
 PGP000198 |
Borde J et al. J Natl Cancer Inst (2020)
|Ext.		 Reported Trait: Breast cancer in CHEK2 mutation carriers between 51 and 60 years of age HR: 1.59 [1.07, 2.35] — — Year of birth, counselling center of origin Only 70 of the original 77 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 70 SNPs used, 7 were proxies R^2>0.8.
PPM017270 PSS010184|
European Ancestry|
200,195 individuals
 PGP000455 |
Spaeth EL et al. Cancer Prev Res (Phila) (2023)
|Ext.		 Reported Trait: breast cancer HR: 1.38 [1.34, 1.42] C-index: 0.628 [0.618, 0.638] — — —
PPM021128 PSS011536|
Ancestry Not Reported|
1,166 individuals
 PGP000616 |
Rosner B et al. Cancer Epidemiol Biomarkers Prev (2020)
|Ext.		 Reported Trait: Incident invasive breast cancer (10- year risk) OR: 1.41 [1.25, 1.59]
β: 0.3432 (0.0696)		 — — — —
PPM021129 PSS011536|
Ancestry Not Reported|
1,166 individuals
 PGP000616 |
Rosner B et al. Cancer Epidemiol Biomarkers Prev (2020)
|Ext.		 Reported Trait: Incident invasive breast cancer (10- year risk) OR: 1.37 [1.21, 1.55]
β: 0.3154 (0.0631)		 — — Questionnaire score, percent mammographic density —
PPM021130 PSS011536|
Ancestry Not Reported|
1,166 individuals
 PGP000616 |
Rosner B et al. Cancer Epidemiol Biomarkers Prev (2020)
|Ext.		 Reported Trait: Incident invasive breast cancer (10- year risk) — AUROC: 0.658 — Age, percent mammographic density, questionnaire score —
PPM021131 PSS011535|
Ancestry Not Reported|
1,336 individuals
 PGP000616 |
Rosner B et al. Cancer Epidemiol Biomarkers Prev (2020)
|Ext.		 Reported Trait: Incident invasive breast cancer (10- year risk) — AUROC: 0.687 — Age, mammographic percent density, questionnaire score —
PPM021132 PSS011536|
Ancestry Not Reported|
1,166 individuals
 PGP000616 |
Rosner B et al. Cancer Epidemiol Biomarkers Prev (2020)
|Ext.		 Reported Trait: Incident invasive breast cancer (10- year risk) — AUROC: 0.659 — Age, BIRADs for mammographic density clasification, questionnaire score —

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
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
 —
PSS010184 — —
[
  • 3,138 cases
  • , 197,057 controls
]
,
0.0 % Male samples
 Range = [40.0, 69.0] years European — UKB —
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
PSS011536 Cases are individuals who were diagnosed with invasive breast cancer. They were free from cancer at the beginning of the study. Mean = 10.0 years
[
  • 533 cases
  • , 633 controls
]
,
0.0 % Male samples
 — Not reported — NHS —
PSS011535 Cases are individuals who were incident diagnosed with invasive breast cancer. Mean = 10.0 years
[
  • 438 cases
  • , 898 controls
]
,
0.0 % Male samples
 — Not reported — MMHS —
PSS001054 All women carried monoallelic protein-truncating germline variants (PTVs) in the CHEK2 gene. 557 of these were the c.1100delc mutation. Cases show individuals with breast cancer. —
[
  • 561 cases
  • , 199 controls
]
,
0.0 % Male samples
 — European — GC-HBOC —