PGS Publication: PGP000198

Publication Information (EuropePMC)
Title Performance of breast cancer polygenic risk scores in 760 female CHEK2 germline mutation carriers.
PubMed ID 33372680(Europe PMC)
doi 10.1093/jnci/djaa203
Publication Date Dec. 29, 2020
Journal J Natl Cancer Inst
Author(s) Borde J, Ernst C, Wappenschmidt B, Niederacher D, Weber-Lassalle K, Schmidt G, Hauke J, Quante AS, Weber-Lassalle N, Horváth J, Pohl-Rescigno E, Arnold N, Rump A, Gehrig A, Hentschel J, Faust U, Dutrannoy V, Meindl A, Kuzyakova M, Wang-Gohrke S, Weber BHF, Sutter C, Volk AE, Giannakopoulou O, Lee A, Engel C, Schmidt MK, Antoniou AC, Schmutzler RK, Kuchenbaecker K, Hahnen E.
Released in PGS Catalog: July 2, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000001
(PRS77_BC)
 PGP000001 |
Mavaddat N et al. J Natl Cancer Inst (2015)
 Breast cancer breast carcinoma 77
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz
PGS000045
(BCPRS_Overall)
 PGP000033 |
Kuchenbaecker KB et al. J Natl Cancer Inst (2017)
 Breast cancer breast carcinoma 88
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000045/ScoringFiles/PGS000045.txt.gz

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) 		Evaluated Score 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
PPM002152 PGS000001
(PRS77_BC)
 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.
PPM002156 PGS000045
(BCPRS_Overall)
 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.
PPM002150 PGS000001
(PRS77_BC)
 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 PGS000001
(PRS77_BC)
 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 PGS000001
(PRS77_BC)
 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 PGS000001
(PRS77_BC)
 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.
PPM002155 PGS000045
(BCPRS_Overall)
 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 PGS000045
(BCPRS_Overall)
 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 PGS000045
(BCPRS_Overall)
 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 PGS000045
(BCPRS_Overall)
 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.

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
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 —