PGS Publication: PGP000248

Publication Information (EuropePMC)
Title Genomic risk prediction of coronary artery disease in women with breast cancer: a prospective cohort study.
PubMed ID 34593009(Europe PMC)
doi 10.1186/s13058-021-01465-0
Publication Date Sept. 30, 2021
Journal Breast Cancer Res
Author(s) Liou L, Kaptoge S, Dennis J, Shah M, Tyrer J, Inouye M, Easton DF, Pharoah PDP.
Released in PGS Catalog: Nov. 4, 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)
PGS000018
(metaGRS_CAD)
PGP000007 |
Inouye M et al. J Am Coll Cardiol (2018)
Coronary artery disease coronary artery disease 1,745,179
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000018/ScoringFiles/PGS000018.txt.gz
PGS000012
(GRS49K)
PGP000005 |
Abraham G et al. Eur Heart J (2016)
Coronary artery disease coronary artery disease 49,310
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000012/ScoringFiles/PGS000012.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
PPM005152 PGS000018
(metaGRS_CAD)
PSS003597|
Multi-ancestry (including European)|
12,413 individuals
PGP000248 |
Liou L et al. Breast Cancer Res (2021)
|Ext.
Reported Trait: Incident coronary artery disease survival in individuals with breast cancer HR: 1.36 [1.23, 1.5] Age SNPs with imputation quality scores of less than 0.3 and ambiguous strand SNPs (A/T and G/C pairs) were excluded from PGS000018.
PPM005153 PGS000018
(metaGRS_CAD)
PSS003596|
European Ancestry|
8,946 individuals
PGP000248 |
Liou L et al. Breast Cancer Res (2021)
|Ext.
Reported Trait: Incident coronary artery disease in individuals with breast cancer HR: 1.36 [1.23, 1.51] Age at diagnosis, genotype array, PCs(1-8) SNPs with imputation quality scores of less than 0.3 and ambiguous strand SNPs (A/T and G/C pairs) were excluded from PGS000018.
PPM005154 PGS000018
(metaGRS_CAD)
PSS003596|
European Ancestry|
8,946 individuals
PGP000248 |
Liou L et al. Breast Cancer Res (2021)
|Ext.
Reported Trait: Incident coronary artery disease in individuals with breast cancer HR: 1.34 [1.21, 1.49] Age at diagnosis, genotype array, PCs(1-8), body mass index, smoking SNPs with imputation quality scores of less than 0.3 and ambiguous strand SNPs (A/T and G/C pairs) were excluded from PGS000018.
PPM005155 PGS000018
(metaGRS_CAD)
PSS003596|
European Ancestry|
8,946 individuals
PGP000248 |
Liou L et al. Breast Cancer Res (2021)
|Ext.
Reported Trait: Incident coronary artery disease in individuals with breast cancer HR: 1.34 [1.21, 1.48] Age at diagnosis, genotype array, PCs(1-8), body mass index, smoking, sociodemographic variables SNPs with imputation quality scores of less than 0.3 and ambiguous strand SNPs (A/T and G/C pairs) were excluded from PGS000018.
PPM005156 PGS000018
(metaGRS_CAD)
PSS003596|
European Ancestry|
8,946 individuals
PGP000248 |
Liou L et al. Breast Cancer Res (2021)
|Ext.
Reported Trait: Incident coronary artery disease in individuals with breast cancer HR: 1.33 [1.2, 1.48] Age at diagnosis, genotype array, PCs(1-8), body mass index, smoking, sociodemographic variables, medical variables SNPs with imputation quality scores of less than 0.3 and ambiguous strand SNPs (A/T and G/C pairs) were excluded from PGS000018.
PPM005157 PGS000018
(metaGRS_CAD)
PSS003596|
European Ancestry|
8,946 individuals
PGP000248 |
Liou L et al. Breast Cancer Res (2021)
|Ext.
Reported Trait: Incident coronary artery disease in individuals with breast cancer HR: 1.33 [1.2, 1.47] Age at diagnosis, genotype array, PCs(1-8), body mass index, smoking, sociodemographic variables, medical variables, oncotherapies SNPs with imputation quality scores of less than 0.3 and ambiguous strand SNPs (A/T and G/C pairs) were excluded from PGS000018.
PPM005158 PGS000012
(GRS49K)
PSS003596|
European Ancestry|
8,946 individuals
PGP000248 |
Liou L et al. Breast Cancer Res (2021)
|Ext.
Reported Trait: Incident coronary artery disease in individuals with breast cancer HR: 1.31 [1.19, 1.44] Age at diagnosis, genotype array, PCs(1-8), body mass index, smoking, sociodemographic variables, medical variables, oncotherapies

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
PSS003596 All individuals had breast cancer. Cases were individuals who suffered incident coronary artery disease (CAD) events. Incident CAD events were defined as a composite endpoint of unstable angina, myocardial infarction, or death due to complications following myocardial infarction according to the International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD-10 codes): I21, I22, I23, I25 and I25.
[
  • 432 cases
  • , 8,514 controls
]
,
0.0 % Male samples
European SEARCH
PSS003597 All individuals had breast cancer. Cases were individuals who suffered incident coronary artery disease (CAD) events. Incident CAD events were defined as a composite endpoint of unstable angina, myocardial infarction, or death due to complications following myocardial infarction according to the International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD-10 codes): I21, I22, I23, I25 and I25. Median = 10.3 years
[
  • 750 cases
  • , 11,663 controls
]
,
0.0 % Male samples
European, African unspecified, Asian unspecified, Not reported European = 11,995, African unspecified = 1, Asian unspecified = 2, Not reported = 413 SEARCH