| Predicted Trait | |
| Reported Trait | HDL cholesterol |
| Mapped Trait(s) | high density lipoprotein cholesterol measurement (EFO_0004612) |
| Additional Trait Information | Continuous lipid trait representing circulating high-density lipoprotein cholesterol (HDL-C) levels. Summary statistics used for polygenic score development were obtained from a multi-ethnic genome-wide association study conducted in the Million Veteran Program (PMID: 30275531). |
| Score Construction | |
| PGS Name | HDL |
| Development Method | |
| Name | Pruning and Thresholding (P+T) |
| Parameters | Polygenic score constructed using clumping and thresholding (P+T) with genome-wide significant variants derived from Million Veteran Program GWAS summary statistics for HDL cholesterol |
| Variants | |
| Original Genome Build | GRCh38 |
| Number of Variants | 482 |
| Effect Weight Type | beta |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000786 |
| Citation (link to publication) | Huang YJ et al. Nat Commun (2026) |
| Ancestry Distribution | |
| Source of Variant Associations (GWAS) | European: 72.4% African: 19.3% Hispanic or Latin American: 8.3% 297,626 individuals (100%) |
| PGS Evaluation | |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST006611 Europe PMC: 30275531 |
215,551 individuals | European | NR |
GWAS Catalog: GCST006611 Europe PMC: 30275531 |
57,332 individuals | African American or Afro-Caribbean | NR |
GWAS Catalog: GCST006611 Europe PMC: 30275531 |
24,743 individuals | Hispanic or Latin American | NR |
|
PGS Performance Metric ID (PPM) |
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 |
|---|---|---|---|---|---|---|---|---|
| PPM030566 | PSS012196| Multi-ancestry (including European)| 42,931 individuals |
PGP000786 | Huang YJ et al. Nat Commun (2026) |
Reported Trait: High-density lipoprotein cholesterol levels | β: 4.15 (0.066) | — | — | sex, age, age^2, BMI, 11 genetic PCs | Effect estimate corresponds to PRS per SD adjusted for genetic PCs. |
| PPM030567 | PSS012196| Multi-ancestry (including European)| 42,931 individuals |
PGP000786 | Huang YJ et al. Nat Commun (2026) |
Reported Trait: High-density lipoprotein cholesterol levels | β: 4.15 (0.066) | — | — | sex, age, age^2, BMI, global ancestry proportions | Effect estimate corresponds to PRS per SD adjusted for global ancestry proportions. |
| PPM030568 | PSS012196| Multi-ancestry (including European)| 42,931 individuals |
PGP000786 | Huang YJ et al. Nat Commun (2026) |
Reported Trait: High-density lipoprotein cholesterol levels | β: 4.15 (0.066) | — | — | sex, age, age^2, BMI, global ePRS | Effect estimate corresponds to residual PRS (rPRS) adjusted for global expected PRS (gePRS). |
| PPM030569 | PSS012196| Multi-ancestry (including European)| 42,931 individuals |
PGP000786 | Huang YJ et al. Nat Commun (2026) |
Reported Trait: High-density lipoprotein cholesterol levels | β: 4.21 (0.066) | — | — | sex, age, age^2, BMI, local ePRS | Effect estimate corresponds to residual PRS (rPRS) adjusted for local expected PRS (lePRS). |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS012196 | — | — | 22,909 individuals | — | European | — | OOA | — |
| PSS012196 | — | — | 10,323 individuals | — | African American or Afro-Caribbean | — | OOA | — |
| PSS012196 | — | — | 8,961 individuals | — | Hispanic or Latin American | — | OOA | — |
| PSS012196 | — | — | 738 individuals | — | Asian unspecified | — | OOA | — |