Whole‐exome sequencing analyses in a Saudi Ischemic Stroke Cohort reveal association signals, and shows polygenic risk scores are related to Modified Rankin Scale Risk

• Published in: Functional & integrative genomics Vol. 23; no. 2; p. 102
• Main Authors: Alkhamis, Fahad A., Alabdali, Majed M., Alsulaiman, Abdulla A., Alamri, Abdullah S., Alali, Rudaynah, Akhtar, Mohammed S., Alsalman, Sadiq A., Cyrus, Cyril, Albakr, Aishah I., Alduhalan, Anas S., Gandla, Divya, Al-Romaih, Khaldoun, Abouelhoda, Mohamed, Loza, Bao-Li, Keating, Brendan, Al-Ali, Amein K.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.06.2023; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Cell Biology; Exome Sequencing; Genes; Genetic Predisposition to Disease; Genome-wide association studies; Genome-Wide Association Study; Genomes; genomics; hospitals; Human Genome Project; Humans; Ischemia; Ischemic Stroke; Life Sciences; Microbial Genetics and Genomics; Original; Original Article; Patients; Plant Genetics and Genomics; Polygenic inheritance; risk; risk assessment; Risk Factors; Saudi Arabia; Single-nucleotide polymorphism; Statistical analysis; Stroke; Stroke - diagnosis; Stroke - epidemiology; Stroke - genetics; Saudi Arabia; Variants; Stroke; Saudi; Recessive; Dominant; Exome sequencing
• DOI: 10.1007/s10142-023-01039-7
• ISSN: 1438-793X; 1438-7948

Ischemic stroke represents a significant societal burden across the globe. Rare high penetrant monogenic variants and less pathogenic common single nucleotide polymorphisms (SNPs) have been described as being associated with risk of diseases. Genetic studies in Saudi Arabian patients offer a greater opportunity to detect rare high penetrant mutations enriched in these consanguineous populations. We performed whole exome sequencing on 387 ischemic stroke subjects from Saudi Arabian hospital networks with up to 20,230 controls from the Saudi Human Genome Project and performed gene burden analyses of variants in 177 a priori loci derived from knowledge-driven curation of monogenic and genome-wide association studies of stroke. Using gene-burden analyses, we observed significant associations in numerous loci under autosomal dominant and/or recessive modelling. Stroke subjects with modified Rankin Scale (mRSs) above 3 were found to carry greater cumulative polygenic risk score (PRS) from rare variants in stroke genes (standardized PRS mean > 0) compared to the population average (standardized PRS mean = 0). However, patients with mRS of 3 or lower had lower cumulative genetic risk from rare variants in stroke genes (OR (95%CI) = 1.79 (1.29–2.49), p  = 0.0005), with the means of standardized PRS at or lower than 0. In conclusion, gene burden testing in Saudi stroke populations reveals a number of statistically significant signals under different disease inheritance models. However, interestingly, stroke subjects with mRS of 3 or lower had lower cumulative genetic risk from rare variants in stroke genes and therefore, determining the potential mRS cutoffs to use for clinical significance may allow risk stratification of this population.