Polygenic Score (PGS) ID: PGS000045

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Dec. 18, 2019
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Score Details

Score Construction
PGS Name BCPRS_Overall
Development Method
Name Known susceptibility loci (genome-wide significant SNPs)
Parameters p<5x10-8, included indpendent SNPs from fine-mapping studies (p < 10-4)
Variants
Original Genome Build GRCh37
Number of Variants 88
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000033
Citation (link to publication) Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
22,627 individuals (100%)
PGS Evaluation
European: 80%
Not Reported: 20%
5 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
PPM000120 PSS000074|
European Ancestry|
1,590 individuals
 PGP000034 |
Lecarpentier J et al. J Clin Oncol (2017)
|Ext.		 Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations OR: 1.36 [1.19, 1.56] AUROC: 0.59 [0.55, 0.63] — 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 PGS predicting Male Breast Cancer are based on association statistics from a Female Breast Cancer GWAS
PPM000106 PSS000070|
European Ancestry|
15,252 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
 Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.14 [1.11, 1.17] C-index: 0.541 [0.53, 0.551] — Country, birth year —
PPM000107 PSS000071|
European Ancestry|
8,211 individuals
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
 Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22 [1.17, 1.28] C-index: 0.566 [0.551, 0.581] — Country, birth year —
PPM002156 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: 1.9 [1.32, 2.75] — — Year of birth, counselling center of origin, PRS*c.1100delC carrier status Only 81 of the original 88 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 81 SNPs used, 7 were proxies R^2>0.8.
PPM002155 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 [1.37, 2.13] — — Year of birth, counselling center of origin Only 81 of the original 88 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 81 SNPs used, 7 were proxies R^2>0.8.
PPM002157 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: 1.59 [1.2, 2.11] — — Year of birth, counselling center of origin Only 81 of the original 88 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 81 SNPs used, 7 were proxies R^2>0.8.
PPM002158 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: 2.07 [1.53, 2.82] — — Year of birth, counselling center of origin Only 81 of the original 88 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 81 SNPs used, 7 were proxies R^2>0.8.
PPM002159 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: 1.56 [1.05, 2.31] — — Year of birth, counselling center of origin Only 81 of the original 88 SNPs were used due to a call rate below 0.95 or significant association with c.1100delC carrier status. Of the 81 SNPs used, 7 were proxies R^2>0.8.
PPM014912 PSS009925|
Ancestry Not Reported|
295 individuals
 PGP000355 |
Borde J et al. BMC Cancer (2022)
|Ext.		 Reported Trait: Breast cancer in BRAC1 PV carriers OR: 1.62 [1.16, 2.31] — — — effective SNP set size of N=77

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
PSS009925 — — 295 individuals,
0.0 % Male samples
 — Not reported — IARC —
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
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 —
PSS000074 Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. —
[
  • 277 cases
  • , 1,313 controls
]
,
100.0 % Male samples
 — European Self-reported European ancestry 37 cohorts
  • BCFR
  • ,BFBOCC
  • ,BRICOH
  • ,CBCS
  • ,CIMBA
  • ,CNIO
  • ,CONSIT
  • ,Chicago
  • ,DEMOKRITOS
  • ,DKFZ
  • ,EMBRACE
  • ,FCCC
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,ILUH
  • ,IOVHBOCS
  • ,IPOBCS
  • ,MAYO
  • ,MSKCC
  • ,MUV
  • ,NCI
  • ,OCGN
  • ,OSU
  • ,OUH
  • ,PBCS
  • ,SWE-BRCA
  • ,UPENN
  • ,UPITT
  • ,VFCTG
  • ,kConFab
 —