Predicted Trait | |
Reported Trait | Atrial fibrillation |
Mapped Trait(s) | atrial fibrillation (EFO_0000275) |
Additional Trait Information | UK Biobank codes: non-cancer codes: 1471, 1483; ICD9: 4273; ICD10: I480-I484, I489 |
Score Construction | |
PGS Name | afib_1 |
Development Method | |
Name | LASSO |
Parameters | To reduce the number of candidate SNPs to a computationally feasible set, a gwas was performed on th... e raw phenotype and the 50,000 snps with smallest p-value were retained. The raw phenotype was regressed on age, sex, and the top 20 UK Biobank PCs and a residual phenotype was then built. The LASSO model was trained using these 50k SNPs and the adjusted phenotype.Show more |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 3,082 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000520 |
Citation (link to publication) | Raben TG et al. Sci Rep (2023) |
Ancestry Distribution | |
Score Development/Training | European: 100% 200,000 individuals (100%) |
PGS Evaluation | European: 100% 1 Sample Sets |
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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— | [ ,
47.0 % Male samples | European | NR | UK Biobank codes: non-cancer codes: 1471, 1483; ICD9: 4273; ICD10: I480-I484, I489 | — | used UK self report 'white' category and then used an adjusted phenotype that includes a regression on the top 20 PCs | — |
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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PPM020119 | PSS011296| European Ancestry| 45,334 individuals | PGP000520 | Raben TG et al. Sci Rep (2023) | Reported Trait: Atrial fibrillation | — | AUROC: 0.73831 | — | year of birth, sex | — |
PPM020120 | PSS011296| European Ancestry| 45,334 individuals | PGP000520 | Raben TG et al. Sci Rep (2023) | Reported Trait: Atrial fibrillation | — | AUROC: 0.73501 | — | year of birth, sex | — |
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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PSS011296 | 22,667 sibling pairs | — | 45,334 individuals | — | European | — | UKB | — |