PGS Publication: PGP000102

Publication Information (EuropePMC)
Title The role of polygenic risk and susceptibility genes in breast cancer over the course of life
PubMed ID 33318493(Europe PMC)
doi 10.1038/s41467-020-19966-5
Publication Date Dec. 14, 2020
Journal Nat Commun
Author(s) Mars N, Widen E, Kerminen S, Meretoja T, Pirinen M, della Briotta Parolo P, Palta P, Palotie A, Kaprio J, Joensuu H, Daly M, Ripatti S, FinnGen.
Released in PGS Catalog: Dec. 15, 2020

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:
Display options:
Ancestry legend
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

PGS Developed 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)
PGS000335
(BC_PRSCS)
 PGP000102 |
Mars N et al. Nat Commun (2020)
 Breast cancer breast carcinoma 1,079,089
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000335/ScoringFiles/PGS000335.txt.gz

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)
PGS000004
(PRS313_BC)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Breast cancer breast carcinoma 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.txt.gz
PGS000332
(PRS_BC)
 PGP000100 |
Mars N et al. Nat Med (2020)
 Breast cancer breast carcinoma 6,390,808
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000332/ScoringFiles/PGS000332.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
PPM001345 PGS000004
(PRS313_BC)
 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
|Ext.		 Reported Trait: Breast cancer HR: 1.55 [1.52, 1.58] — — 10 ancestry PCs, batch, age as time scale 260/313 variants in the PRS are polymorphic in FinnGen
PPM001347 PGS000004
(PRS313_BC)
 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
|Ext.		 Reported Trait: Breast cancer OR: 1.61 [1.57, 1.64] — — Age, 10 ancestry PCs, batch 260/313 variants in the PRS are polymorphic in FinnGen
PPM001346 PGS000332
(PRS_BC)
 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
|Ext.		 Reported Trait: Breast cancer HR: 1.63 [1.6, 1.67] — — 10 ancestry PCs, batch, age as time scale —
PPM001348 PGS000332
(PRS_BC)
 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
|Ext.		 Reported Trait: Breast cancer OR: 1.71 [1.67, 1.75] — — Age, 10 ancestry PCs, batch —
PPM000903 PGS000335
(BC_PRSCS)
 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
 Reported Trait: Breast cancer OR: 1.8 [1.76, 1.84] — — Age, 10 ancestry PCs, batch —
PPM000902 PGS000335
(BC_PRSCS)
 PSS000450|
European Ancestry|
122,978 individuals
 PGP000102 |
Mars N et al. Nat Commun (2020)
 Reported Trait: Breast cancer HR: 1.71 [1.68, 1.75] — — 10 ancestry PCs, batch, age as time scale —

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
PSS000450 Breast cancer cases were identified through the Finnish Cancer Registry with diagnosis C50 (International Classification of Diseases for Oncology, 3rd Edition; ICD-O-3), from the drug reimbursement registry by selecting individuals with a reimbursement code for breast cancer, and from the death registry with ICD-10 C50. —
[
  • 8,401 cases
  • , 114,577 controls
]
,
0.0 % Male samples
 Mean Age (At The End Of Follow-Up) = 58.5 years
IQR = [45.1, 72.2] years		 European
(Finnish)		 — FinnGen —