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(Variants and weights)

Polygenic Score (PGS) ID: PGS000038

Predicted Trait

Reported Trait: Stroke
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): stroke

Score Details

Name: PRS90

Original Genome Build: NR
Number of Variants: 90

PGS Development Method: Clumping + Thresholding
PGS Development Details/Relevant Parameters: P < 1×10−5; Independent SNPs were clumped based selected using the following thresholds: r2 < 0.05 or 1000 Kb apart using plink

Citation: Rutten-Jacobs LC et al. BMJ (2018) | PGS Catalog Publication ID: PGP000026

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST006906
PubMed: 29531354
446,696 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000090 PSS000057 Rutten-Jacobs LC et al. (2018) Reported Trait: Incident stroke HR (High [top 33%] vs. Low [bottom 33%] of genetic risk): 1.35 [1.21 - 1.5] age, sex, 10 PCs of genetic ancestry, genotyping batch The best performing PRS (e.g. C+T thresholds) were selected based on this sample set, as well as being used for the evaluation.
PPM000092 PSS000058 Abraham G et al. (2019) Ext. Reported Trait: Ischaemic stroke before age 75 HR: 1.13 [1.1 - 1.17] Sex, genotyping chip, 10 PCs

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000057 Incident stroke in was defined based on the UK Biobank (UKB) algorithm, based on medical history and linkage to data on hospital admissions and mortality. The authors also subtyped ischaemic stroke, intracerebral haemorrhage, or subarachnoid haemorrhage. UKB Participants with genetic data were excluded from the analysis based on the following criteria: failing genetic quality control (missingness > 5%, sex mismatch, excessive heterozygosity), having a history of stroke or myocardial infarction (MI), self-report of stroke or MI, missing lifestyle information. 306,473 individuals
[ 2,077 cases, 304,396 controls]
44.59 %% Male samples
European Unrelated White British subset of UKB participants UKB
PSS000058 Prevalent and incident Ischaemic stroke; defined in http://biobank.ndph.ox.ac.uk/showcase/docs/alg_outcome_stroke.pdf 395,393 individuals
[ 3,075 cases, 392,318 controls]
45.70 %% Male samples
European UKB Validation set