Genetic association analysis of age of ischemic stroke onset: a caveat

Joanna von Berg, Patrick F. McArdle, Paavo Häppölä, Charles Kooperberg, SiGN consortium, FinnGen, Women’s Health Initiative, Steven J. Kittner, Braxton D. Mitchell, Jeroen de Ridder, Sander W. van der Laan.

Abstract

Large genome-wide association studies (GWAS) employing case-control study designs have now identified tens of loci associated with ischemic stroke (IS). As a complement to these studies, we performed GWAS in a case-only design to identify loci influencing age at onset (AAO) of ischemic stroke. Analyses were conducted in a Discovery cohort of 10,857 ischemic stroke cases under a linear regression framework. We meta-analyzed all SNPs with p-value < 1x10^-5 in a sex-combined or sex-stratified analysis using summary data from two additional Replication cohorts. In the women-only meta-analysis, we detected significant evidence for association of AAO with rs429358 - an exonic variant in APOE that encodes for the APOE-Є4 allele. Each copy of the rs429358:T>C allele was associated with a 1.29 years earlier stroke AOO (meta p-value = 2.48x10^-11).

This APOE variant has previously been associated with increased mortality, but not with ischemic stroke AAO. We therefore hypothesized that the association with AAO may reflect a survival bias attributable to an age-related decline in mortality among APOE-Є4 carriers and having no association to stroke AAO per se. Using a simulation study, we found that a variant associated with overall mortality might indeed be detected with an AAO analysis. A variant with a two-fold increase on mortality risk would lead to an observed effect of AAO that is comparable to what we found. In conclusion, we detected a robust association of the APOE locus with stroke AAO and provided simulations to suggest that this association may be unrelated to ischemic stroke per se but related to a general survival bias.

Where do I start?

You can load this project in RStudio by opening the file called 'AAO_IschemicStroke.git.Rproj'.

Project structure

File	Description	Usage
README.md	Description of project	Human editable
LICENSE	User permissions	Read only
AAO_IschemicStroke.git.Rproj	Project file	Loads project
.worcs	WORCS metadata YAML	Read only
renv.lock	Reproducible R environment	Read only

1. Parsing_GWASSumStats.Rmd | Notebook to plot GWAS data | Human editable
2. AssociationPlots.Rmd | Notebook to create regional plots | Human editable
3. SimulationPlot.Rmd | Notebook for the simulation analysis | Human editable
4. forest.poster.sign.Rmd | Notebook to generate the forest plot | Human editable _AAO_archived | Some scribble-scripts | Human editable AAO | Results and plots | Human editable finemap | Results from finemapping; not used; available offline | Human editable images | Project images | Human editable meta | Results from the meta-GWAS | Human editable meta_discovery | Discovery results | Human editable meta_other_stuff | Results from meta-analysis; raw input; not used; available offline | Human editable simulation_data | Simulation data | Human editable scripts | Simulation plot | Human editable targets | Targets from this study | Human editable

Data

All the input data and individual cohort GWAS summary statistics are available through our collaborators (FinnGen and WHI), and for SiGN through dbGaP: [link here]

The summary statistics from the meta-analysis in SiGN are available through dataverseNL [link here] and GWAS Catalog [link here].

The lookups in the MEGASTROKE data, FinnGen, and WHI are in the meta-folder.

Reproducibility

This project uses the Workflow for Open Reproducible Code in Science (WORCS) to ensure transparency and reproducibility. The workflow is designed to meet the principles of Open Science throughout a research project.

To learn how WORCS helps researchers meet the TOP-guidelines and FAIR principles, read the preprint at https://osf.io/zcvbs/

WORCS: Advice for authors

• To get started with worcs, see the setup vignette
• For detailed information about the steps of the WORCS workflow, see the workflow vignette

WORCS: Advice for readers

Please refer to the vignette on reproducing a WORCS project for step by step advice.

Acknowledgements

This work was supported by NIH grants R01 NS100178 and R01 NS105150 from the U.S. National Institutes of Health. JdR is supported by a Vidi Fellowship (639.072.715) from the Dutch Organization for Scientific Research (Nederlandse Organisatie voor Wetenschappelijk Onderzoek, NWO). SJK is additionally supported by the Department of Veterans Affairs RR&D N1699-R and BX004672-01A1. SWvdL is funded through EU H2020 TO_AITION (grant number: 848146).

We are thankful for the support of the Netherlands CardioVascular Research Initiative of the Netherlands Heart Foundation (CVON 2011/B019 and CVON 2017-20: Generating the best evidence-based pharmaceutical targets for atherosclerosis [GENIUS I&II]), the ERA-CVD program ‘druggable-MI-targets’ (grant number: 01KL1802), and the Leducq Fondation ‘PlaqOmics’.

The Women’s Health Initiatives (WHI) program was funded by the National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services through contracts 75N92021D00001, 75N92021D00002, 75N92021D00003, 75N92021D00004, and 75N92021D00005.

The framework was based on the WORCS package.

Changes log

Version:      v1.0.2
Last update:  2023-0-21
Written by:   Sander W. van der Laan (s.w.vanderlaan-2[at]umcutrecht.nl).
Description:  Script to get some figures for AAO.
Minimum requirements: R version 3.4.3 (2017-06-30) -- 'Single Candle', Mac OS X El Capitan

Changes log
* v1.0.3 Fixed genetic effects and power figure for clarity.
* v1.0.2 Textual fixes. Changes to the funding.
* v1.0.1 Additional clarifications on data availability. Updates to plots. Updates to available results.
* v1.0.0 Initial version. 

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Copyright (c) 1979-2023 Sander W. van der Laan | s.w.vanderlaan [at] gmail [dot] com.

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