PGS Publication: PGP000351

Publication Information (EuropePMC)
Title Genetic Aspects of Mammographic Density Measures Associated with Breast Cancer Risk.
PubMed ID 35681745(Europe PMC)
doi 10.3390/cancers14112767
Publication Date June 2, 2022
Journal Cancers (Basel)
Author(s) Li S, Nguyen TL, Nguyen-Dumont T, Dowty JG, Dite GS, Ye Z, Trinh HN, Evans CF, Tan M, Sung J, Jenkins MA, Giles GG, Hopper JL, Southey MC.
Released in PGS Catalog: Aug. 3, 2022

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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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

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
PGS000005
(PRS313_ERpos)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 ER-positive breast cancer estrogen-receptor positive breast cancer 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000005/ScoringFiles/PGS000005.txt.gz
PGS000006
(PRS313_ERneg)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 ER-negative breast cancer estrogen-receptor negative breast cancer 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000006/ScoringFiles/PGS000006.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
PPM014886 PGS000004
(PRS313_BC)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cumulus Mammogram Risk Scores β: 0.061 [0.017, 0.105] — — first 10 principal components —
PPM014887 PGS000004
(PRS313_BC)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cumulus percent Mammogram Risk Scores β: 0.06 [0.016, 0.104] — — first 10 principal components —
PPM014888 PGS000004
(PRS313_BC)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Altocumulus Mammogram Risk Scores β: 0.081 [0.037, 0.125] — — first 10 principal components —
PPM014889 PGS000004
(PRS313_BC)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cirrocumulus Mammogram Risk Scores β: 0.058 [0.016, 0.101] — — first 10 principal components —
PPM014890 PGS000006
(PRS313_ERneg)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cumulus Mammogram Risk Scores β: 0.059 [0.015, 0.103] — — first 10 principal components —
PPM014892 PGS000006
(PRS313_ERneg)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Altocumulus Mammogram Risk Scores β: 0.068 [0.024, 0.112] — — first 10 principal components —
PPM014893 PGS000006
(PRS313_ERneg)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cirrocumulus Mammogram Risk Scores β: 0.046 [0.003, 0.089] — — first 10 principal components —
PPM014894 PGS000006
(PRS313_ERneg)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cumulus-white Mammogram Risk Scores β: 0.045 [0.002, 0.089] — — first 10 principal components —
PPM014895 PGS000005
(PRS313_ERpos)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cumulus Mammogram Risk Scores β: 0.056 [0.012, 0.1] — — first 10 principal components —
PPM014896 PGS000005
(PRS313_ERpos)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cumulus percent Mammogram Risk Scores β: 0.055 [0.011, 0.099] — — first 10 principal components —
PPM014897 PGS000005
(PRS313_ERpos)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Altocumulus Mammogram Risk Scores β: 0.078 [0.034, 0.121] — — first 10 principal components —
PPM014898 PGS000005
(PRS313_ERpos)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cirrocumulus Mammogram Risk Scores β: 0.056 [0.014, 0.099] — — first 10 principal components —
PPM014891 PGS000006
(PRS313_ERneg)
 PSS009919|
Ancestry Not Reported|
2,559 individuals
 PGP000351 |
Li S et al. Cancers (Basel) (2022)
|Ext.		 Reported Trait: Cumulus percent Mammogram Risk Scores β: 0.065 [0.021, 0.109] — — first 10 principal components —

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
PSS009919 — — 2,559 individuals,
0.0 % Male samples
 Mean = 54.0 years
Sd = 8.4 years		 Not reported — NR AMDTSS