Whole-exome sequencing of a Saudi epilepsy cohort reveals association signals in known and potentially novel loci

Abdulrahman H Al Anazi; Ahmed S Ammar; Mahmoud Al-Hajj; Cyril Cyrus; Danah Aljaafari; Iname Khoda; Ahmed K Abdelfatah; Abdullah A Alsulaiman; Firas Alanazi; Rawan Alanazi; Divya Gandla; Hetal Lad; Samar Barayan; Brendan J Keating; Amein K Al-Ali

doi:10.1186/s40246-022-00444-6

Whole-exome sequencing of a Saudi epilepsy cohort reveals association signals in known and potentially novel loci

Hum Genomics. 2022 Dec 20;16(1):71. doi: 10.1186/s40246-022-00444-6.

Authors

Affiliations

¹ Department of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
² Department of Neurosurgery, King Fahd Hospital, Alhafof, Saudi Arabia.
³ Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, 31441, Dammam, Saudi Arabia.
⁴ Department of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
⁵ Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
⁶ Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, 31441, Dammam, Saudi Arabia. aalali@iau.edu.sa.

Abstract

Background: Epilepsy, a serious chronic neurological condition effecting up to 100 million people globally, has clear genetic underpinnings including common and rare variants. In Saudi Arabia, the prevalence of epilepsy is high and caused mainly by perinatal and genetic factors. No whole-exome sequencing (WES) studies have been performed to date in Saudi Arabian epilepsy cohorts. This offers a unique opportunity for the discovery of rare genetic variants impacting this disease as there is a high rate of consanguinity among large tribal pedigrees.

Results: We performed WES on 144 individuals diagnosed with epilepsy, to interrogate known epilepsy-related genes for known and functional novel variants. We also used an American College of Medical Genetics (ACMG) guideline-based variant prioritization approach in an attempt to discover putative causative variants. We identified 32 potentially causative pathogenic variants across 30 different genes in 44/144 (30%) of these Saudi epilepsy individuals. We also identified 232 variants of unknown significance (VUS) across 101 different genes in 133/144 (92%) subjects. Strong enrichment of variants of likely pathogenicity was observed in previously described epilepsy-associated loci, and a number of putative pathogenic variants in novel loci are also observed.

Conclusion: Several putative pathogenic variants in known epilepsy-related loci were identified for the first time in our population, in addition to several potential new loci which may be prioritized for further investigation.

Keywords: Epilepsy; Neurological conditions; Saudi Arabia; Variants; WES.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Epilepsy* / diagnosis
Epilepsy* / epidemiology
Epilepsy* / genetics
Exome Sequencing
Exome* / genetics
Genetic Predisposition to Disease
Humans
Pedigree
Saudi Arabia / epidemiology