| Predicted Trait | |
| Reported Trait | Coronary heart disease |
| Mapped Trait(s) | coronary artery disease (EFO_0001645) |
| Score Construction | |
| PGS Name | CHD_PRSCS |
| Development Method | |
| Name | PRS-CS |
| Parameters | PRS-CS-auto, 1000G European sample (N = 503) as the external LD reference panel |
| Variants | |
| Original Genome Build | GRCh38 |
| Number of Variants | 1,090,048 |
| Effect Weight Type | beta |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000261 |
| Citation (link to publication) | Tamlander M et al. Commun Biol (2022) |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST003116 Europe PMC: 26343387 |
3,139 individuals | African American or Afro-Caribbean | 41 cohorts
|
GWAS Catalog: GCST003116 Europe PMC: 26343387 |
4,095 individuals | Hispanic or Latin American | 41 cohorts
|
GWAS Catalog: GCST003116 Europe PMC: 26343387 |
11,323 individuals | East Asian | 41 cohorts
|
GWAS Catalog: GCST003116 Europe PMC: 26343387 |
25,557 individuals | South Asian | 41 cohorts
|
GWAS Catalog: GCST003116 Europe PMC: 26343387 |
141,217 individuals | European | 41 cohorts
|
GWAS Catalog: GCST003116 Europe PMC: 26343387 |
2,268 individuals | Greater Middle Eastern (Middle Eastern, North African or Persian) | 40 cohorts
|
|
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 |
|---|---|---|---|---|---|---|---|---|
| PPM009286 | PSS007689| European Ancestry| 343,672 individuals |
PGP000261 | Tamlander M et al. Commun Biol (2022) |
Reported Trait: Prevalent coronary heart disease | OR: 1.77 [1.73, 1.8] | AUROC: 0.811 [0.808, 0.815] | — | year of birth, sex | — |
| PPM009276 | PSS007681| European Ancestry| 309,154 individuals |
PGP000261 | Tamlander M et al. Commun Biol (2022) |
Reported Trait: Coronary heart disease (incident and prevalent) | OR: 1.56 [1.53, 1.58] | AUROC: 0.871 [0.869, 0.873] | — | year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array | — |
| PPM009278 | PSS007687| European Ancestry| 343,672 individuals |
PGP000261 | Tamlander M et al. Commun Biol (2022) |
Reported Trait: Coronary heart disease (incident and prevalent) | OR: 1.72 [1.7, 1.75] | AUROC: 0.792 [0.789, 0.795] | — | year of birth, sex | — |
| PPM009282 | PSS007688| European Ancestry| 332,370 individuals |
PGP000261 | Tamlander M et al. Commun Biol (2022) |
Reported Trait: Incident coronary heart disease | OR: 1.61 [1.57, 1.65] | AUROC: 0.756 [0.751, 0.761] | — | year of birth, sex | — |
| PPM009284 | PSS007683| European Ancestry| 309,154 individuals |
PGP000261 | Tamlander M et al. Commun Biol (2022) |
Reported Trait: Prevalent coronary heart disease | OR: 1.59 [1.57, 1.62] | AUROC: 0.869 [0.867, 0.871] | — | year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array | — |
| PPM009280 | PSS007682| European Ancestry| 291,720 individuals |
PGP000261 | Tamlander M et al. Commun Biol (2022) |
Reported Trait: Incident coronary heart disease | OR: 1.44 [1.41, 1.47] | AUROC: 0.913 [0.911, 0.916] | — | year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS007681 | Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2019, whichever came first. | Median = 15.3 years IQR = [7.8, 22.6] years |
[ ,
43.8 % Male samples |
Mean (Age At Baseline) = 53.2 years Sd = 17.4 years |
European (Finnish) |
— | FinnGen | — |
| PSS007682 | Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2019, whichever came first. | — | [ ,
42.2 % Male samples |
Mean (Age At Baseline) = 52.2 years Sd = 17.3 years |
European (Finnish) |
— | FinnGen | — |
| PSS007683 | Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2019, whichever came first. | — | [ ,
43.8 % Male samples |
Mean (Age At Baseline) = 53.2 years Sd = 17.4 years |
European (Finnish) |
— | FinnGen | — |
| PSS007687 | Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first. | Median = 10.7 years IQR = [8.6, 11.6] years |
[ ,
46.3 % Male samples |
Mean (Age At Baseline) = 57.4 years Sd = 8.0 years |
European (British) |
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. | UKB | — |
| PSS007688 | Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first. | — | [ ,
45.1 % Male samples |
Mean (Age At Baseline) = 57.2 years Sd = 8.0 years |
European (British) |
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. | UKB | — |
| PSS007689 | Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first. | — | [ ,
46.3 % Male samples |
Mean (Age At Baseline) = 57.4 years Sd = 8.0 years |
European (British) |
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. | UKB | — |