PGS Publication: PGP000239

Publication Information (EuropePMC)
Title Combining Clinical and Polygenic Risk Improves Stroke Prediction Among Individuals With Atrial Fibrillation.
PubMed ID 34029116(Europe PMC)
doi 10.1161/circgen.120.003168
Publication Date June 15, 2021
Journal Circ Genom Precis Med
Author(s) O'Sullivan JW, Shcherbina A, Justesen JM, Turakhia M, Perez M, Wand H, Tcheandjieu C, Clarke SL, Rivas MA, Ashley EA.
Released in PGS Catalog: Oct. 7, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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PGS Developed By This Publication

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)
PGS000911
(PRS_IS)
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Ischemic stroke stroke,
Ischemic stroke		 530,933
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000911/ScoringFiles/PGS000911.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

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
PPM002960 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases OR: 1.14 [1.06, 1.23] — — Age at recruitment, sex, UK Biobank array type, PCs(1-10) —
PPM002961 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases OR: 1.14 [1.06, 1.23] AUROC: 0.605 [0.583, 0.626] — Age at recruitment, sex, UK Biobank array type, PCs(1-10), presence of warfarin prescription —
PPM002962 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases who had not been prescribed warfarin OR: 1.14 [1.05, 1.24] — — Age at recruitment, sex, UK Biobank array type, PCs(1-10) —
PPM002963 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases OR: 1.14 [1.06, 1.23] — — Age at recruitment, sex, UK Biobank array type, PCs(1-10), cumulative CHA2DS2-VASc score —
PPM002964 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases OR: 1.14 — — Age at recruitment, sex, UK Biobank array type, PCs(1-10), individual components of CHA2DS2-VASc score —
PPM002965 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases HR: 1.13 [1.04, 1.21] C-index: 0.56 [0.54, 0.58] — Sex, UK Biobank array, PCs(1-10) —
PPM002966 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases HR: 1.14 [1.01, 1.23] C-index: 0.56 [0.54, 0.58] — Sex, age, UK Biobank array, PCs(1-10) —
PPM002967 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases who had not been prescribed warfarin HR: 1.13 [1.04, 1.22] C-index: 0.57 [0.54, 0.59] — Sex, UK Biobank array, PCs(1-10) —
PPM002968 PGS000911
(PRS_IS)
 PSS001445|
European Ancestry|
15,929 individuals
 PGP000239 |
O'Sullivan JW et al. Circ Genom Precis Med (2021)
 Reported Trait: Ischemic stroke in atrial fibrillation cases — C-index: 0.61 [0.58, 0.63] — Sex, UK Biobank array, PCs(1-10), cumulative CHA2DS2-VASc score —

Evaluated Samples

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
PSS001445 All individuals had a history of incident atrial fibrillation (AF) following enrollment. 2,310 individuals were taking warfarin. Cases were individuals with ischemic stroke (IS). IS was defined uisng the UKB codes: 131368, 42008. Of the 2,310 individuals taking warfarin, 93 were individuals with ischemic stroke (cases). Median = 7.0 years
[
  • 684 cases
  • , 15,245 controls
]
,
66.7 % Male samples
 European — UKB —