Clinical exome sequencing identifies novel gene variants associated with ischemic stroke in the Saudi Tabuk population

Abdullah Hamadi^1*Rashid Mir^1*Osama Alamer¹Mohammed Alasseiri¹Waseem AlZamzami¹Sael Alatawi¹Mohammad A Alanazi¹Atif Abdulwahab A. Oyouni²Abeer Al Tuwaijri³Saleh Althenayyan³Hassan Madkhali⁴Raed Alserihi⁵Mamdoh S. Moawadh¹

• ¹Medical laboratory technology, Faculty of applied medical sciences, University of Tabuk, Tabuk, Saudi Arabia
• ²Department of Biology, FAS, Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
• ³Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
• ⁴Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al Kharj, Saudi Arabia
• ⁵Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Hematology Research Unit (HRU), King Fahad Medical Research Center (KFMRC),, King Abdulaziz University, Jeddah, Saudi Arabia

Background: Variants linked to the risk of ischaemic stroke have been discovered through genome-wide association studies (GWASs). These variations frequently have little consequences that lack apparent biological significance. Hence, these findings demonstrate that exome sequencing can be highly relevant to stroke, even though stroke is a complex phenotype with various diseases and risk factors. Methodology: In this case-control investigation, we used ARMS genotyping to investigate the distribution of polymorphic variations in genes associated with stroke susceptibility. In addition to examine the novel gene variations associated with ischaemic stroke we utilized the Illumina NovaSeq 6000 platform for whole-exome sequencing (WES). Results: Results identified 11 novel gene variants in the GSTT4 gene by Targeted Whole-Exome Sequencing, including one deletion GSTT4p.Asn232LysfsTer6, one insertion c.688_689insCG, and 9 SNVs c.699T>C, c.701C>G, c.708G>T, c.710T>G, c.712A>G, c.712A>G, c.718A>T, c.719G>A, c.721A>T, c.722G>T in the ischaemic stroke patients. We also identified several rare, intermediate, and most common gene variants in cholesterol associated genes LDLR, LDLRAD2, LDLRAD3, APOA2, APOA3, APOA4, APOA5, and PCSK9. Also, several common gene variants were reported in MTHFR, KLF14, eNOS3, and ACE by whole-exome sequencing. Furthermore, the eNOS3-GG and eNOS3-GT genotypes were associated with susceptibility to ischaemic stroke (OR=1.95, P<0.05). Conclusion: This case-control study identified eleven novel GSTT4 variants and several known polymorphisms associated with ischemic stroke risk in Saudi patients. These findings highlight population-specific genetic factors that warrant further functional and large-scale validation.