| Publication Information (EuropePMC) | |
| Title | A polygenic biomarker to identify patients with severe hypercholesterolemia of polygenic origin. |
| PubMed ID | 32307928(Europe PMC) |
| doi | 10.1002/mgg3.1248 |
| Publication Date | April 19, 2020 |
| Journal | Mol Genet Genomic Med |
| Author(s) | Leal LG, Hoggart C, Jarvelin MR, Herzig KH, Sternberg MJE, David A. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000875 (PGS36_LDLc) |
PGP000221 | Leal LG et al. Mol Genet Genomic Med (2020) |
LDL cholesterol | low density lipoprotein cholesterol measurement | 36 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000875/ScoringFiles/PGS000875.txt.gz |
| 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) |
|---|---|---|---|---|---|---|
| PGS000814 (GRS12_LDLc) |
PGP000200 | Talmud PJ et al. Lancet (2013) |
LDL cholesterol | low density lipoprotein cholesterol measurement | 16 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000814/ScoringFiles/PGS000814.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM002500 | PGS000875 (PGS36_LDLc) |
PSS001124| European Ancestry| 4,787 individuals |
PGP000221 | Leal LG et al. Mol Genet Genomic Med (2020) |
Reported Trait: Low-density lipoprotein cholesterol | — | — | R²: 0.08 | Age, gender, body mass index, ancestry differences captured by the first two components from multidimensional scaling | — |
| PPM002501 | PGS000875 (PGS36_LDLc) |
PSS001124| European Ancestry| 4,787 individuals |
PGP000221 | Leal LG et al. Mol Genet Genomic Med (2020) |
Reported Trait: Severe hypercholesterolemia | — | — | Risk Ratio (RR, top 30% vs bottom 30%): 4.8 [2.6, 8.9] | — | — |
| PPM002502 | PGS000875 (PGS36_LDLc) |
PSS001124| European Ancestry| 4,787 individuals |
PGP000221 | Leal LG et al. Mol Genet Genomic Med (2020) |
Reported Trait: Low-density lipoprotein cholesterol | — | AUROC: 0.67 | — | — | — |
| PPM002503 | PGS000814 (GRS12_LDLc) |
PSS001124| European Ancestry| 4,787 individuals |
PGP000221 | Leal LG et al. Mol Genet Genomic Med (2020) |Ext. |
Reported Trait: Low-density lipoprotein cholesterol | — | AUROC: 0.65 | — | — | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS001124 | Individuals with severe hypercholesterolemia (HC) had a LDL-C level > 4.9 mmol/L. 124 individuals had severe HC, based on this criteria. Individuals with intermediate HC had a LDL-C level 3.0 ≤ LDL‐C ≤ 4.9 mmol/L. 1927 individuals had intermediate HC, based on this criteria. Individuals classified as having normal LDL-C levels had LDL-C levels < 3.0 mmol/L. 2733 individuals had normal LDL-C levels, based on this criteria. | — | 4,787 individuals, 48.0 % Male samples |
Mean = 31.0 years Sd = 0.2 years |
European | — | NFBC | — |