| Publication Information (EuropePMC) | |
| Title | Cardiovascular Disease Risk Assessment Using Traditional Risk Factors and Polygenic Risk Scores in the Million Veteran Program. |
| PubMed ID | 37133828(Europe PMC) |
| doi | 10.1001/jamacardio.2023.0857 |
| Publication Date | June 1, 2023 |
| Journal | JAMA Cardiol |
| Author(s) | Vassy JL, Posner DC, Ho YL, Gagnon DR, Galloway A, Tanukonda V, Houghton SC, Madduri RK, McMahon BH, Tsao PS, Damrauer SM, O'Donnell CJ, Assimes TL, Casas JP, Gaziano JM, Pencina MJ, Sun YV, Cho K, Wilson PWF. |
| 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) |
|---|---|---|---|---|---|---|
| PGS002244 (ldpred_cad) |
PGP000271 | Mars N et al. Cell Genom (2022) |
Coronary artery disease | coronary artery disease | 6,576,338 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002244/ScoringFiles/PGS002244.txt.gz | |
| PGS002724 (GIGASTROKE_iPGS_EUR) |
PGP000333 | Mishra A et al. Nature (2022) |
Ischemic stroke | Ischemic stroke, stroke |
1,213,574 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002724/ScoringFiles/PGS002724.txt.gz |
|
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM020273 | PGS002724 (GIGASTROKE_iPGS_EUR) |
PSS011318| African Ancestry| 18,505 individuals |
PGP000536 | Vassy JL et al. JAMA Cardiol (2023) |Ext. |
Reported Trait: Incident ischemic stroke | HR: 1.05 [0.95, 1.17] | — | — | age, sex, and principal components of genetic ancestry | — |
| PPM020274 | PGS002724 (GIGASTROKE_iPGS_EUR) |
PSS011319| Hispanic or Latin American Ancestry| 6,785 individuals |
PGP000536 | Vassy JL et al. JAMA Cardiol (2023) |Ext. |
Reported Trait: Incident ischemic stroke | HR: 1.08 [0.85, 1.36] | — | — | age, sex, and principal components of genetic ancestry | — |
| PPM020275 | PGS002724 (GIGASTROKE_iPGS_EUR) |
PSS011320| European Ancestry| 53,861 individuals |
PGP000536 | Vassy JL et al. JAMA Cardiol (2023) |Ext. |
Reported Trait: Incident ischemic stroke | HR: 1.15 [1.08, 1.21] | — | — | age, sex, and principal components of genetic ancestry | — |
| PPM020276 | PGS002244 (ldpred_cad) |
PSS011318| African Ancestry| 18,505 individuals |
PGP000536 | Vassy JL et al. JAMA Cardiol (2023) |Ext. |
Reported Trait: Incident myocardial infarction | HR: 1.1 [1.02, 1.19] | — | — | age, sex, and principal components of genetic ancestry | — |
| PPM020277 | PGS002244 (ldpred_cad) |
PSS011319| Hispanic or Latin American Ancestry| 6,785 individuals |
PGP000536 | Vassy JL et al. JAMA Cardiol (2023) |Ext. |
Reported Trait: Incident myocardial infarction | HR: 1.26 [1.09, 1.46] | — | — | age, sex, and principal components of genetic ancestry | — |
| PPM020278 | PGS002244 (ldpred_cad) |
PSS011320| European Ancestry| 53,861 individuals |
PGP000536 | Vassy JL et al. JAMA Cardiol (2023) |Ext. |
Reported Trait: Incident myocardial infarction | HR: 1.23 [1.18, 1.29] | — | — | age, sex, and principal components of genetic ancestry | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS011318 | — | — | 18,505 individuals, 81.9 % Male samples |
Mean = 55.4 years Sd = 11.8 years |
African American or Afro-Caribbean | — | MVP | — |
| PSS011319 | — | — | 6,785 individuals, 86.5 % Male samples |
Mean = 52.6 years Sd = 14.8 years |
Hispanic or Latin American | — | MVP | — |
| PSS011320 | — | — | 53,861 individuals, 88.2 % Male samples |
Mean = 59.3 years Sd = 13.8 years |
European | — | MVP | — |