| Publication Information (EuropePMC) | |
| Title | Polygenic Scores and Preclinical Cardiovascular Disease in Individuals With HIV: Insights From the REPRIEVE Trial. |
| PubMed ID | 38533953(Europe PMC) |
| doi | 10.1161/jaha.123.033413 |
| Publication Date | March 27, 2024 |
| Journal | J Am Heart Assoc |
| Author(s) | Zou RS, Ruan Y, Truong B, Bhattacharya R, Lu MT, Karády J, Bernardo R, Finneran P, Hornsby W, Fitch KV, Ribaudo HJ, Zanni MV, Douglas PS, Grinspoon SK, Patel AP, Natarajan P. |
| 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) |
|---|---|---|---|---|---|---|
| PGS003725 (GPS_Mult) |
PGP000466 | Patel AP et al. Nat Med (2023) |
Coronary artery disease | coronary artery disease | 1,296,172 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003725/ScoringFiles/PGS003725.txt.gz | |
| PGS002654 (biochemistry_LDLdirect.PolyFun-pred) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
LDL cholesterol | low density lipoprotein cholesterol measurement | 274,585 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002654/ScoringFiles/PGS002654.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM023040 | PGS003725 (GPS_Mult) |
PSS012103| Multi-ancestry (including European)| 663 individuals |
PGP000763 | Zou RS et al. J Am Heart Assoc (2024) |Ext. |
Reported Trait: Stenosis over 50% | OR: 2.39 [1.48, 3.85] | — | — | age, sex, and the first 10 principal components of ancestry | — |
| PPM023041 | PGS003725 (GPS_Mult) |
PSS012103| Multi-ancestry (including European)| 663 individuals |
PGP000763 | Zou RS et al. J Am Heart Assoc (2024) |Ext. |
Reported Trait: Visible non calcified plaque or with vulnerable features | OR: 1.45 [1.23, 1.72] | — | — | age, sex, and the first 10 principal components of ancestry | — |
| PPM023042 | PGS002654 (biochemistry_LDLdirect.PolyFun-pred) |
PSS012103| Multi-ancestry (including European)| 663 individuals |
PGP000763 | Zou RS et al. J Am Heart Assoc (2024) |Ext. |
Reported Trait: Plaque presence (on coronary computed tomography angiography) | OR: 1.21 [1.01, 1.44] | — | — | age, sex, and the first 10 principal components of ancestry | — |
| PPM023043 | PGS002654 (biochemistry_LDLdirect.PolyFun-pred) |
PSS012103| Multi-ancestry (including European)| 663 individuals |
PGP000763 | Zou RS et al. J Am Heart Assoc (2024) |Ext. |
Reported Trait: partially calcified plaque | OR: 1.21 [1.01, 1.45] | — | — | age, sex, and the first 10 principal components of ancestry | — |
| PPM023039 | PGS003725 (GPS_Mult) |
PSS012103| Multi-ancestry (including European)| 663 individuals |
PGP000763 | Zou RS et al. J Am Heart Assoc (2024) |Ext. |
Reported Trait: Plaque presence (on coronary computed tomography angiography) | OR: 1.42 [1.2, 1.68] | — | — | age, sex, and the first 10 principal components of 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 |
|---|---|---|---|---|---|---|---|---|
| PSS012103 | — | — | 277 individuals | — | African unspecified | — | REPRIEVE | — |
| PSS012103 | — | — | 379 individuals | — | European | — | REPRIEVE | — |
| PSS012103 | — | — | 6 individuals | — | East Asian | — | REPRIEVE | — |
| PSS012103 | — | — | 1 individuals | — | South Asian | — | REPRIEVE | — |