AS576 - Whole genome sequence analysis of ischemic stroke in the Women's Health Initiative

Investigator Names and Contact Information

Alexander Reiner (apreiner@uw.edu)

Introduction/Intent

Specific Aims:

Aim 1. Discover, replicate, and functionally characterize new loci (particularly rare or low frequency coding and non-coding regulatory variants) for ischemic stroke (and its subtypes) using whole genome sequencing (WGS) and imputation. Discovery will be performed in ~4,000 incident ischemic stroke cases and over 5,000 controls from WHI with WGS through TOPMed. Single variant and gene-based tests will be performed. Replication will be performed through state-of-the art WGS-based GWAS imputation in additional ischemic stroke cases and controls obtained through UKBiobank and the SiGN and METASTROKE GWAS consortia. Given that statistical power is limited for testing rare variants individually, we will additionally perform ‘biologically meaningful’ aggregate or gene-based sets testing of rare variants by linking non-coding regulatory elements to gene targets. To additionally enhance our statistical power, we will stratify the single variant and gene-based association tests according to prior hypotheses and stringency of significance threshold. We will perform: (1) an agnostic discovery scan using the typically stringent genome-wide threshold of significance (P = 5 x 10-8); (2) a more biologically-targeted (and less stringent) analysis of rare variant across 100 genomic regions previously associated with stroke and related atherosclerotic and thrombo-embolic disorders.

Aim 2. To identify and assess the biologic mechanism of newly validated genetic loci in ischemic stroke pathogenesis through a multi-tiered proteomic approach: Test ischemic stroke-associated variants for association with:

• (1) A rich set of CVD risk factors and other phenotypic markers available in WHI;
• (2) A comprehensive proteomic, metabolomics, and methylation panel, measured on all subjects within the WHI TOPMed study, as well as RNAseq data and a second set of the various ‘omics measurements measured at the LLS time-point for those subjects within the TOPMed cohort that were part of the LLS.
• (3) By combining the results of association analyses of stroke ~ genotype, biomarker ~ genotype, and stroke ~ biomarker, assess the mechanistic relationship between genotype, intermediate biomarker phenotype, and stroke outcome.

Exploratory Aim. To discover, replicate, and functionally characterize new loci for hemorrhagic stroke using 1000 incident cases and 5,000 controls from WHI with WGS through TOPMed. Replication will be performed in an additional 2000 hemorrhagic cases and 2000 controls from the NHGRI Complex Disease Sequencing Program. We will conduct single variant and aggregated association tests. To the extent that there is an overlap in loci with ischemic stroke, we will assess the biological mechanism for genetic loci in hemorrhagic stroke similar as in Aim 2 for ischemic stroke.