Short report: Targeted analysis of whole exome sequencing data in Indian cryptogenic stroke patients

Abstract

Cryptogenic stroke (CS) is an ischemic stroke of unknown cause with increasing incidence in India. Common and rare genetic variants have been associated with the risk of stroke. We carried out targeted analysis of whole exome sequencing on a small cohort of 16 CS patients to determine whether rare coding variants in genes previously associated with stroke could play a role in India. Variants were filtered for coverage ([≥]15x) and minor allele frequency ([≤]0.01). Potential pathogenic variants were classified according to ACMG guidelines, and targeted analysis performed by filtering for these variants in a panel of 220 stroke-related genes. Enrichr and STRING were used to look for enrichment of gene sets and pathways in putative deleterious (PHRED-scaled CADD scores [≥]15) variants identified in CS cases. One pathogenic and 26 variants of uncertain significance were identified in 19 genes in CS patients. Enrichr showed significant enrichment for gene-sets in phenotypes (e.g. hemorrhage; abnormal blood coagulation) and pathways (e.g. common pathway of fibrin clot formation; response to elevated platelet cytosolic Ca2+) that could contribute to CS, indicating specific genes (e.g. IGA2B, F13A1, F5, ATP7A, JAG1, PKD1, PMM2, GLA) to be targeted for follow-up.