Polygenic Score (PGS) ID: PGS000038

Predicted Trait
Reported Trait Stroke
Mapped Trait(s) stroke (EFO_0000712)
Released in PGS Catalog: Dec. 18, 2019
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Score Details

Score Construction
PGS Name PRS90
Development Method
Name Clumping and Thresholding (C+T)
Parameters P < 1×10−5; Independent SNPs were clumped based selected using the following thresholds: r2 < 0.05 or 1000 Kb apart using plink
Variants
Original Genome Build NR
Number of Variants 90
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000026
Citation (link to publication) Rutten-Jacobs LC et al. BMJ (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
446,696 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST006906
Europe PMC: 29531354
 446,696 individuals European NR

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) 		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
PPM000090 PSS000057|
European Ancestry|
306,473 individuals
 PGP000026 |
Rutten-Jacobs LC et al. BMJ (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|
European Ancestry|
395,393 individuals
 PGP000027 |
Abraham G et al. Nat Commun (2019)
|Ext.		 Reported Trait: Ischaemic stroke before age 75 HR: 1.13 [1.1, 1.17] — — Sex, genotyping chip, 10 PCs —

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
PSS000058 Prevalent and incident Ischaemic stroke; defined in http://biobank.ndph.ox.ac.uk/showcase/docs/alg_outcome_stroke.pdf Mean = 6.3 years
Sd = 1.9 years
[
  • 3,075 cases
  • , 392,318 controls
]
,
45.7 % Male samples
 Mean = 54.3 years European — UKB Validation set
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. Median = 7.1 years
[
  • 2,077 cases
  • , 304,396 controls
]
,
44.59 % Male samples
 Mean = 56.7 years
Sd = 7.9 years		 European Unrelated White British subset of UKB participants UKB —