| Publication Information (EuropePMC) | |
| Title | Integration of polygenic and gut metagenomic risk prediction for common diseases. |
| PubMed ID | 38528230(Europe PMC) |
| doi | 10.1038/s43587-024-00590-7 |
| Publication Date | March 25, 2024 |
| Journal | Nat Aging |
| Author(s) | Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vázquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna AS, Knight R, Méric G, Inouye M. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000018 (metaGRS_CAD) |
PGP000007 | Inouye M et al. J Am Coll Cardiol (2018) |
Coronary artery disease | coronary artery disease | 1,745,179 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000018/ScoringFiles/PGS000018.txt.gz | |
| PGS000662 (GRS.PCa.269) |
PGP000122 | Conti DV et al. Nat Genet (2021) |
Prostate cancer | prostate carcinoma | 269 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000662/ScoringFiles/PGS000662.txt.gz |
| PGS000036 (gePS_T2D) |
PGP000023 | Mahajan A et al. Nat Genet (2018) |
Type 2 diabetes (T2D) | type 2 diabetes mellitus | 171,249 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000036/ScoringFiles/PGS000036.txt.gz | |
| PGS000334 (GRSfull_22) |
PGP000101 | Zhang Q et al. Nat Commun (2020) |
Late-onset Alzheimer’s disease | late-onset Alzheimer's disease | 22 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000334/ScoringFiles/PGS000334.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM022979 | PGS000018 (metaGRS_CAD) |
PSS012083| European Ancestry| 5,093 individuals |
PGP000754 | Liu Y et al. Nat Aging (2024) |Ext. |
Reported Trait: Incident coronary artery disease | HR: 1.68 [1.5, 1.88] β: 0.51613 |
— | — | Baseline age, BMI, systolic BP, total cholesterol, HDL, smoking, exercise, prevelant diabetes, family history, gut microbiome score | — |
| PPM022980 | PGS000036 (gePS_T2D) |
PSS012085| European Ancestry| 5,297 individuals |
PGP000754 | Liu Y et al. Nat Aging (2024) |Ext. |
Reported Trait: Incident type 2 diabetes | HR: 1.41 [1.29, 1.54] β: 0.34536 |
— | — | Baseline age, BMI, systolic BP, total cholesterol, HDL, smoking, exercise, prevelant diabetes, family history, gut microbiome score | — |
| PPM022981 | PGS000334 (GRSfull_22) |
PSS012082| European Ancestry| 5,347 individuals |
PGP000754 | Liu Y et al. Nat Aging (2024) |Ext. |
Reported Trait: Incident Alzheimer's disease | HR: 1.93 [1.73, 2.15] β: 0.65554 |
— | — | Baseline age, BMI, systolic BP, total cholesterol, HDL, smoking, exercise, prevelant diabetes, family history, gut microbiome score | — |
| PPM022982 | PGS000662 (GRS.PCa.269) |
PSS012084| European Ancestry| 2,464 individuals |
PGP000754 | Liu Y et al. Nat Aging (2024) |Ext. |
Reported Trait: Incident prostate cancer | HR: 1.72 [1.46, 2.02] β: 0.53998 |
— | — | Baseline age, BMI, systolic BP, total cholesterol, HDL, smoking, exercise, prevelant diabetes, family history, gut microbiome score | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS012082 | — | — | [
|
— | European (Finnish) |
— | FINRISK | — |
| PSS012083 | — | — | [
|
— | European (Finnish) |
— | FINRISK | — |
| PSS012084 | — | — | [
|
— | European (Finnish) |
— | FINRISK | — |
| PSS012085 | — | — | [
|
— | European (Finnish) |
— | FINRISK | — |