Predicted Trait | |
Reported Trait | Coronary Artery Disease |
Mapped Trait(s) | coronary artery disease (EFO_0001645) |
Score Construction | |
PGS Name | CAD_PRS_LDpred_UKB_Pub1 |
Development Method | |
Name | LDpred |
Parameters | LDpred v1.0.08 / Rho parameter = 0.01 / LD reference panel = 1000 Genomes Consortium, 503 European P... articipants. Variants with info score R2 < 0.3 (i.e. quality of imputation), minor allele frequency (MAF) < 0.01, multi-allelic, insertion or deletions and with MAF discrepancies > 10% between all datasets were excluded. Only SNPs included in the Phase 3 HapMap Consortium (~1.2 million) were kept for the PRS derivation.Show more |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 1,146,511 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000532 |
Citation (link to publication) | Manikpurage HD et al. Circ Genom Precis Med (2021) |
Study Identifiers
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Sample Numbers
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Sample Ancestry
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Cohort(s)
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GWAS Catalog: GCST003116 Europe PMC: 26343387 | 141,217 individuals | European | NR |
GWAS Catalog: GCST003116 Europe PMC: 26343387 | 3,139 individuals | African American or Afro-Caribbean | NR |
GWAS Catalog: GCST003116 Europe PMC: 26343387 | 4,095 individuals | Hispanic or Latin American | NR |
GWAS Catalog: GCST003116 Europe PMC: 26343387 | 25,557 individuals | South Asian | NR |
GWAS Catalog: GCST003116 Europe PMC: 26343387 | 2,268 individuals | Greater Middle Eastern (Middle Eastern, North African or Persian) | NR |
GWAS Catalog: GCST003116 Europe PMC: 26343387 | 11,323 individuals | East Asian | NR |
Study Identifiers
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Sample Numbers
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Sample Ancestry
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Cohort(s)
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Phenotype Definitions & Methods
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Age of Study Participants
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Participant Follow-up Time
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Additional Ancestry Description
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Additional Sample/Cohort Information
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— | [ ,
42.0 % Male samples | European (White British) | UKB | To define prevalent CAD, we selected participants with ICD-10 codes for MI (I21.X, I22.X, I23.X, I24... .1, or I25.2), for other acute ischemic heart disease (I24.0, I24.8-9) and for atherosclerotic / chronic ischemic heart disease (I25.0-25.1, I25.5-25.9). Procedure codes for coronary artery bypass grafting (K40.1-40.4, K41.1-41.4, K45.1-45.5), for coronary angioplasty, with or without stenting (K49.1-49.2, K49.8-49.9, K50.2, K75.1-75.4, K75.8-75.9) were also added to the CAD definition.Show more | Mean = 55.97 years | — | — | — |
PGS Performance Metric ID (PPM) |
PGS Sample Set ID (PSS) |
Performance Source
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Trait
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PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
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Covariates Included in the Model
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PGS Performance: Other Relevant Information |
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PPM020258 | PSS011313| European Ancestry| 403,422 individuals | PGP000532 | Manikpurage HD et al. Circ Genom Precis Med (2021) | Reported Trait: Prevalent Coronary Artery Disease | OR: 1.56 [1.56, 1.58] | AUROC: 0.766 | R²: 0.158 | Age, Sex and Genetic Principal Components (1 to 10) | — |
PPM020259 | PSS011313| European Ancestry| 403,422 individuals | PGP000532 | Manikpurage HD et al. Circ Genom Precis Med (2021) | Reported Trait: Prevalent Myocardial Infarction | OR: 1.63 [1.6, 1.65] | AUROC: 0.772 | R²: 0.129 | Age, Sex and Genetic Principal Components (1 to 10) | — |
PPM020260 | PSS011313| European Ancestry| 403,422 individuals | PGP000532 | Manikpurage HD et al. Circ Genom Precis Med (2021) | Reported Trait: Prevalent Myocardial Infarction and Coronary Revascularization procedure | OR: 1.73 [1.7, 1.76] | AUROC: 0.789 | R²: 0.162 | Age, Sex and Genetic Principal Components (1 to 10) | — |
PPM020261 | PSS011313| European Ancestry| 403,422 individuals | PGP000532 | Manikpurage HD et al. Circ Genom Precis Med (2021) | Reported Trait: Incident Myocardial Infarction | HR: 1.53 [1.49, 1.56] | C-index: 0.729 | — | Age, Sex and Genetic Principal Components (1 to 10) | — |
PPM020262 | PSS011313| European Ancestry| 403,422 individuals | PGP000532 | Manikpurage HD et al. Circ Genom Precis Med (2021) | Reported Trait: Mortality | HR: 1.08 [1.06, 1.09] | — | — | Age, Sex and Genetic Principal Components (1 to 10) | — |
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods
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Participant Follow-up Time
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Sample Numbers
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Age of Study Participants
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Sample Ancestry
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Additional Ancestry Description
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Cohort(s)
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Additional Sample/Cohort Information
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PSS011313 | To define prevalent CAD, we selected participants with ICD-10 codes for MI (I21.X, I22.X, I23.X, I24... .1, or I25.2), for other acute ischemic heart disease (I24.0, I24.8-9) and for atherosclerotic / chronic ischemic heart disease (I25.0-25.1, I25.5-25.9). Procedure codes for coronary artery bypass grafting (K40.1-40.4, K41.1-41.4, K45.1-45.5), for coronary angioplasty, with or without stenting (K49.1-49.2, K49.8-49.9, K50.2, K75.1-75.4, K75.8-75.9) were also added to the CAD definition.Show more | Mean = 11.0 years | [ ,
46.0 % Male samples | Mean = 56.93 years | European (White British) | — | UKB | — |