| Publication Information (EuropePMC) | |
| Title | Comparison of genetic risk prediction models to improve prediction of coronary heart disease in two large cohorts of the MONICA/KORA study. |
| PubMed ID | 34082474(Europe PMC) |
| doi | 10.1002/gepi.22389 |
| Publication Date | June 3, 2021 |
| Journal | Genet Epidemiol |
| Author(s) | Bauer A, Zierer A, Gieger C, Büyüközkan M, Müller-Nurasyid M, Grallert H, Meisinger C, Strauch K, Prokisch H, Roden M, Peters A, Krumsiek J, Herder C, Koenig W, Thorand B, Huth C. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000818 (GRS_Metabo) |
PGP000202 | Bauer A et al. Genet Epidemiol (2021) |
Coronary heart disease | coronary artery disease | 138 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000818/ScoringFiles/PGS000818.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) |
|---|---|---|---|---|---|---|
| PGS000013 (GPS_CAD) |
PGP000006 | Khera AV et al. Nat Genet (2018) |
Coronary artery disease | coronary artery disease | 6,630,150 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM002180 | PGS000818 (GRS_Metabo) |
PSS001064| European Ancestry| 1,939 individuals |
PGP000202 | Bauer A et al. Genet Epidemiol (2021) |
Reported Trait: Incident coronary heart disease | HR: 1.2341 [1.1137, 1.3676] | — | — | — | — |
| PPM002181 | PGS000818 (GRS_Metabo) |
PSS001064| European Ancestry| 1,939 individuals |
PGP000202 | Bauer A et al. Genet Epidemiol (2021) |
Reported Trait: Incident coronary heart disease | HR: 1.2126 [1.0766, 1.3659] | — | — | Age, sex, survey | — |
| PPM002182 | PGS000013 (GPS_CAD) |
PSS001063| European Ancestry| 2,909 individuals |
PGP000202 | Bauer A et al. Genet Epidemiol (2021) |Ext. |
Reported Trait: Incident coronary heart disease | — | C-index: 0.573 [0.5254, 0.6212] | — | — | Only 6,481,934 SNPs from PGS000013 were utilised. SNPs were not included due to imputation quality R^2 < 0.3 |
| PPM002178 | PGS000818 (GRS_Metabo) |
PSS001063| European Ancestry| 2,909 individuals |
PGP000202 | Bauer A et al. Genet Epidemiol (2021) |
Reported Trait: Incident coronary heart disease | — | C-index: 0.7571 [0.7234, 0.7908] | — | Age, sex, survey | — |
| PPM002179 | PGS000818 (GRS_Metabo) |
PSS001063| European Ancestry| 2,909 individuals |
PGP000202 | Bauer A et al. Genet Epidemiol (2021) |
Reported Trait: Incident coronary heart disease | — | C-index: 0.792 [0.7622, 0.8219] | — | Age, sex, survey, Framingham risk score (diabetes status, current and former smoking status, systolic blood pressure, antihypertensive medication, HDL cholesterol, total cholesterol) | — |
| PPM002183 | PGS000013 (GPS_CAD) |
PSS001063| European Ancestry| 2,909 individuals |
PGP000202 | Bauer A et al. Genet Epidemiol (2021) |Ext. |
Reported Trait: Incident coronary heart disease | — | C-index: 0.7752 [0.7443, 0.8029] | — | Age, sex, survey | Only 6,481,934 SNPs from PGS000013 were utilised. SNPs were not included due to imputation quality R^2 < 0.3 |
| PPM002184 | PGS000013 (GPS_CAD) |
PSS001063| European Ancestry| 2,909 individuals |
PGP000202 | Bauer A et al. Genet Epidemiol (2021) |Ext. |
Reported Trait: Incident coronary heart disease | — | C-index: 0.8012 [0.7775, 0.8353] | — | Age, sex, survey, Framingham risk score (diabetes status, current and former smoking status, systolic blood pressure, antihypertensive medication, HDL cholesterol, total cholesterol) | Only 6,481,934 SNPs from PGS000013 were utilised. SNPs were not included due to imputation quality R^2 < 0.3 |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS001064 | Cases were individuals with incident coronary heart disesase (CHD). The outcome CHD was a combined endpoint of nonfatal myocardial infarction as well as coronary death and sudden death (International Classification of Disease 9th Revision: 410–414 and 798). Until December 2000, the diagnosis of a major, nonfatal myocardial infarction and coronary death was based on the MONICA algorithm in which a diagnosis of a major CHD event was based on symptoms, cardiac enzymes (creatine kinase, aspartate aminotransferase, and lactate dehydrogenase), serial changes from 12‐lead electrocardiograms (ECGs) evaluated by Minnesota coding, necropsy results and history of CHD in fatal cases. Since January 1, 2001, the diagnosis of myocardial infarction was based on the European Society of Cardiology and American College of Cardiology criteria. Incident events were identified through follow‐up questionnaires or through the MONICA/KORA myocardial infarction registry, which monitors the occurrence of all in‐ and out of‐hospital fatal and nonfatal myocardial infarctions among the 25–74‐year‐old inhabitants of the study region. Initially identified self‐reported incident cases and the self‐reported date of diagnosis not covered by the MONICA/KORA myocardial infarction registry, were validated by hospital records or by contacting the patient's treating physician. Deaths from myocardial in- farction were validated by death certificates, autopsy reports, chart reviews, or information from the last treating physician. | Median = 14.0 years IQR = [10.3, 14.0] years |
[ ,
53.06 % Male samples |
— | European | — | KORA | — |
| PSS001063 | Cases were individuals with incident coronary heart disesase (CHD). The outcome CHD was a combined endpoint of nonfatal myocardial infarction as well as coronary death and sudden death (International Classification of Disease 9th Revision: 410–414 and 798). Until December 2000, the diagnosis of a major, nonfatal myocardial infarction and coronary death was based on the MONICA algorithm in which a diagnosis of a major CHD event was based on symptoms, cardiac enzymes (creatine kinase, aspartate aminotransferase, and lactate dehydrogenase), serial changes from 12‐lead electrocardiograms (ECGs) evaluated by Minnesota coding, necropsy results and history of CHD in fatal cases. Since January 1, 2001, the diagnosis of myocardial infarction was based on the European Society of Cardiology and American College of Cardiology criteria. Incident events were identified through follow‐up questionnaires or through the MONICA/KORA myocardial infarction registry, which monitors the occurrence of all in‐ and out of‐hospital fatal and nonfatal myocardial infarctions among the 25–74‐year‐old inhabitants of the study region. Initially identified self‐reported incident cases and the self‐reported date of diagnosis not covered by the MONICA/KORA myocardial infarction registry, were validated by hospital records or by contacting the patient's treating physician. Deaths from myocardial in- farction were validated by death certificates, autopsy reports, chart reviews, or information from the last treating physician. | Median = 14.0 years IQR = [14.0, 14.0] years |
[ ,
48.1 % Male samples |
— | European | — | KORA | — |