The copy number variation and stroke (CaNVAS) risk and outcome study

Abstract

Background and purpose: The role of copy number variation (CNV) variation in stroke susceptibility and outcome has yet to be explored. The Copy Number Variation and Stroke (CaNVAS) Risk and Outcome study addresses this knowledge gap.

Methods: Over 24,500 well-phenotyped IS cases, including IS subtypes, and over 43,500 controls have been identified, all with readily available genotyping on GWAS and exome arrays, with case measures of stroke outcome. To evaluate CNV-associated stroke risk and stroke outcome it is planned to: 1) perform Risk Discovery using several analytic approaches to identify CNVs that are associated with the risk of IS and its subtypes, across the age-, sex- and ethnicity-spectrums; 2) perform Risk Replication and Extension to determine whether the identified stroke-associated CNVs replicate in other ethnically diverse datasets and use biomarker data (e.g. methylation, proteomic, RNA, miRNA, etc.) to evaluate how the identified CNVs exert their effects on stroke risk, and lastly; 3) perform outcome-based Replication and Extension analyses of recent findings demonstrating an inverse relationship between CNV burden and stroke outcome at 3 months (mRS), and then determine the key CNV drivers responsible for these associations using existing biomarker data.

Results: The results of an initial CNV evaluation of 50 samples from each participating dataset are presented demonstrating that the existing GWAS and exome chip data are excellent for the planned CNV analyses. Further, some samples will require additional considerations for analysis, however such samples can readily be identified, as demonstrated by a sample demonstrating clonal mosaicism.

Conclusion: The CaNVAS study will cost-effectively leverage the numerous advantages of using existing case-control data sets, exploring the relationships between CNV and IS and its subtypes, and outcome at 3 months, in both men and women, in those of African and European-Caucasian descent, this, across the entire adult-age spectrum.

Fig 1. CaNVAS study timeline (2020–2025).

Fig 2. Histogram showing the number of CNV-calls by PennCNV (X-axis) and the number of samples (Y-axis) from 4 CaNVAS centers.

Fig 3. Visualization of all SNPs of a sample.

Upper panel shows for each SNP the signal intensity, lower panel shows for each SNP the distribution of the signal across the two alleles. This case from Barcelona (Identifier 4800000347) is a man: the signal intensity of X-chromosomal SNPs is reduced (i.e. there is only one copy of the X-chromosome, compared to two copies of the autosomes. As there is only one X, there are no heterozygous SNPs. As a consequence, the mid-line of the allelic distribution (representing the heterozygous SNPs) is empty.

Fig 4. Detail of Fig 3 (arrow) region demonstrating a deletion in one of the two chromosomes.

Fig 5. SIREN case with an additional copy of the genomic region at the tip of the long arm of chromosome 18 (duplication).

Fig 6. Zoom-in of the SIREN case with a CNV duplication in 18q.

Fig 7. SIREN participant sample with clonal mosaicism.