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.
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

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)
PGS005092
(PGS_prscsx)
 PGP000684 |
Abramowitz SA et al. JAMA (2024)
 Coronary artery disease coronary artery disease 1,279,502
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005092/ScoringFiles/PGS005092.txt.gz
PGS005091
(PGS_LDP2Auto)
 PGP000684 |
Abramowitz SA et al. JAMA (2024)
 Coronary artery disease coronary artery disease 1,428,772
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005091/ScoringFiles/PGS005091.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
PPM022178 PGS005091
(PGS_LDP2Auto)
 PSS011830|
Multi-ancestry (including European)|
171,095 individuals
 PGP000684 |
Abramowitz SA et al. JAMA (2024)
 Reported Trait: Prevalent coronary heart disease OR: 1.452 [1.427, 1.477] AUROC: 0.776 Brier score: 0.0825 Age, sex Scores in model are PCA-normalized
PPM022179 PGS005091
(PGS_LDP2Auto)
 PSS011832|
Multi-ancestry (including European)|
53,092 individuals
 PGP000684 |
Abramowitz SA et al. JAMA (2024)
 Reported Trait: Prevalent coronary heart disease OR: 1.374 [1.343, 1.406] AUROC: 0.8 Brier score: 0.143 Age, sex, first 5 PCs Scores in model are PCA-normalized
PPM022180 PGS005091
(PGS_LDP2Auto)
 PSS011831|
Multi-ancestry (including European)|
41,193 individuals
 PGP000684 |
Abramowitz SA et al. JAMA (2024)
 Reported Trait: Prevalent coronary heart disease OR: 1.547 [1.506, 1.59] AUROC: 0.791 Brier score: 0.1405 Age, sex Scores in model are PCA-normalized
PPM022181 PGS005092
(PGS_prscsx)
 PSS011830|
Multi-ancestry (including European)|
171,095 individuals
 PGP000684 |
Abramowitz SA et al. JAMA (2024)
 Reported Trait: Prevalent coronary heart disease OR: 1.407 [1.384, 1.43] AUROC: 0.774 Brier score: 0.0828 Age, sex Scores in model are PCA-normalized
PPM022182 PGS005092
(PGS_prscsx)
 PSS011832|
Multi-ancestry (including European)|
53,092 individuals
 PGP000684 |
Abramowitz SA et al. JAMA (2024)
 Reported Trait: Prevalent coronary heart disease OR: 1.384 [1.353, 1.416] AUROC: 0.801 Brier score: 0.1425 Age, sex, first 5 PCs Scores in model are PCA-normalized
PPM022183 PGS005092
(PGS_prscsx)
 PSS011831|
Multi-ancestry (including European)|
41,193 individuals
 PGP000684 |
Abramowitz SA et al. JAMA (2024)
 Reported Trait: Prevalent coronary heart disease OR: 1.562 [1.522, 1.604] AUROC: 0.793 Brier score: 0.1402 Age, sex Scores in model are PCA-normalized

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
PSS011832 Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease —
[
  • 8,137 cases
  • , 25,577 controls
]
 — European — UCLA —
PSS011832 Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease —
[
  • 731 cases
  • , 1,951 controls
]
 — African unspecified — UCLA —
PSS011832 Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease —
[
  • 1,510 cases
  • , 6,006 controls
]
 — Hispanic or Latin American — UCLA —
PSS011832 Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease —
[
  • 967 cases
  • , 3,992 controls
]
 — East Asian — UCLA —
PSS011832 Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease —
[
  • 168 cases
  • , 640 controls
]
 — South Asian — UCLA —
PSS011832 Chronic condition warehouse definitions for myocardial infarction and ischemic heart disease —
[
  • 999 cases
  • , 2,414 controls
]
 — Not reported — UCLA —
PSS011830 410, 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 —
PSS011830 410, 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 —
PSS011830 410, 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 —
PSS011830 410, 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 —
PSS011830 410, 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 —
PSS011830 410, 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 —
PSS011831 410, 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 —
PSS011831 410, 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 —
PSS011831 410, 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 —
PSS011831 410, 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 —
PSS011831 410, 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 —
PSS011831 410, 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 —