PGS Publication: PGP000684

Publication Information (EuropePMC)
Title Evaluating Performance and Agreement of Coronary Heart Disease Polygenic Risk Scores.
PubMed ID 39549270(Europe PMC)
doi 10.1001/jama.2024.23784
Publication Date Nov. 16, 2024
Journal JAMA
Author(s) Abramowitz SA, Boulier K, Keat K, Cardone KM, Shivakumar M, DePaolo J, Judy R, Bermudez F, Mimouni N... , Neylan C, Kim D, Rader DJ, Ritchie MD, Voight BF, Pasaniuc B, Levin MG, Damrauer SM, Penn Medicine BioBank.Show more
Released in PGS Catalog: Nov. 21, 2024

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

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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)
PGS005091
(PGS_LDP2Auto)
PGP000684 |
Abramowitz SA et al. JAMA (2024)
Coronary artery diseasecoronary artery disease1,428,772
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005091/ScoringFiles/PGS005091.txt.gz
PGS005092
(PGS_prscsx)
PGP000684 |
Abramowitz SA et al. JAMA (2024)
Coronary artery diseasecoronary artery disease1,279,502
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005092/ScoringFiles/PGS005092.txt.gz
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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.

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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
PPM022178PGS005091
(PGS_LDP2Auto)
PSS011830|
Multi-ancestry (including European)|
171,095 individuals
PGP000684 |
Abramowitz SA et al. JAMA (2024)
Reported Trait: Prevalent coronary heart diseaseOR: 1.452 [1.427, 1.477]AUROC: 0.776Brier score: 0.0825Age, sexScores in model are PCA-normalized
PPM022179PGS005091
(PGS_LDP2Auto)
PSS011832|
Multi-ancestry (including European)|
53,092 individuals
PGP000684 |
Abramowitz SA et al. JAMA (2024)
Reported Trait: Prevalent coronary heart diseaseOR: 1.374 [1.343, 1.406]AUROC: 0.8Brier score: 0.143Age, sex, first 5 PCsScores in model are PCA-normalized
PPM022180PGS005091
(PGS_LDP2Auto)
PSS011831|
Multi-ancestry (including European)|
41,193 individuals
PGP000684 |
Abramowitz SA et al. JAMA (2024)
Reported Trait: Prevalent coronary heart diseaseOR: 1.547 [1.506, 1.59]AUROC: 0.791Brier score: 0.1405Age, sexScores in model are PCA-normalized
PPM022181PGS005092
(PGS_prscsx)
PSS011830|
Multi-ancestry (including European)|
171,095 individuals
PGP000684 |
Abramowitz SA et al. JAMA (2024)
Reported Trait: Prevalent coronary heart diseaseOR: 1.407 [1.384, 1.43]AUROC: 0.774Brier score: 0.0828Age, sexScores in model are PCA-normalized
PPM022182PGS005092
(PGS_prscsx)
PSS011832|
Multi-ancestry (including European)|
53,092 individuals
PGP000684 |
Abramowitz SA et al. JAMA (2024)
Reported Trait: Prevalent coronary heart diseaseOR: 1.384 [1.353, 1.416]AUROC: 0.801Brier score: 0.1425Age, sex, first 5 PCsScores in model are PCA-normalized
PPM022183PGS005092
(PGS_prscsx)
PSS011831|
Multi-ancestry (including European)|
41,193 individuals
PGP000684 |
Abramowitz SA et al. JAMA (2024)
Reported Trait: Prevalent coronary heart diseaseOR: 1.562 [1.522, 1.604]AUROC: 0.793Brier score: 0.1402Age, sexScores in model are PCA-normalized
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Evaluated Samples

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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
PSS011830410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 11,344 cases
  • , 89,149 controls
]
—European—AllofUs—
PSS011830410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 3,558 cases
  • , 32,032 controls
]
—African unspecified—AllofUs—
PSS011830410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 2,268 cases
  • , 27,533 controls
]
—Hispanic or Latin American—AllofUs—
PSS011830410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 134 cases
  • , 1,612 controls
]
—South Asian—AllofUs—
PSS011830410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 132 cases
  • , 1,865 controls
]
—East Asian—AllofUs—
PSS011830410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 153 cases
  • , 1,315 controls
]
—Greater Middle Eastern (Middle Eastern, North African or Persian)—AllofUs—
PSS011831410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 6,761 cases
  • , 21,323 controls
]
—European—PMB—
PSS011831410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 1,932 cases
  • , 7,898 controls
]
—African unspecified—PMB—
PSS011831410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 312 cases
  • , 1,565 controls
]
—Hispanic or Latin American—PMB—
PSS011831410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 88 cases
  • , 462 controls
]
—South Asian—PMB—
PSS011831410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 70 cases
  • , 514 controls
]
—East Asian—PMB—
PSS011831410, 411, 412, 413, 41, V45.81 (ICD-9), I21, I22, I24, Z95.1, Z98.61, I20.0 (ICD-10)—
[
  • 52 cases
  • , 216 controls
]
—Greater Middle Eastern (Middle Eastern, North African or Persian)—PMB—
PSS011832Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease—
[
  • 8,137 cases
  • , 25,577 controls
]
—European—UCLA—
PSS011832Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease—
[
  • 731 cases
  • , 1,951 controls
]
—African unspecified—UCLA—
PSS011832Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease—
[
  • 1,510 cases
  • , 6,006 controls
]
—Hispanic or Latin American—UCLA—
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