Whole exome sequencing of an Algerian Parkinson’s disease cohort: an exploratory study identifying rare variants in putative candidate genes

Abstract

Parkinson’s disease (PD), a complex neurodegenerative disorder, is increasingly prevalent, with a strong genetic component. While environmental factors contribute, the exact cause remains elusive. Understanding PD’s genetic basis is vital for advancing research and treatment. This study seeks to investigate the genetic diversity of Parkinson’s disease in the Algerian population using whole exome sequencing (WES), with the goal of identifying rare variants across genes potentially associated with the disease. Whole exome sequencing (WES) was performed on a cohort of 19 Algerian patients with clinically confirmed Parkinson’s disease, including 8 patients with a positive family history. Variant annotation and functional effect prediction were performed using SnpEff, in conjunction with multiple reference genomic databases. Variant calling results were stored in Variant Call Format (VCF). Variants were classified according to their minor allele frequency (MAF): rare variants were defined as those with a MAF between 0.1% and 1%, while novel variants were defined as those with a MAF ≤ 0.1% or absent from all queried reference databases. Whole exome sequencing analysis identified 73 variants distributed across 22 genes in 19 Algerian patients with Parkinson’s disease. Following prioritization, nine variants were detected across six candidate genes (DDOST, AUP1, SNORD66, TRPM7, ORC6, and GLUD2), whose association with Parkinson’s disease had not been previously reported in North African populations. These genes are involved in several cellular functions, including protein homeostasis, DNA repair, cellular metabolism, and oxidative stress response. Among them, GLUD2 emerges as a particularly compelling candidate requiring functional validation for future investigations. This preliminary study highlights the genetic diversity of Parkinson’s disease in the Algerian population and underscores the value of whole exome sequencing for the identification of rare variants in underrepresented populations. The findings suggest potential novel research avenues that may contribute to expanding knowledge of the genetic architecture of the disease. Replication studies and functional validation will be required to confirm the biological and clinical relevance of the identified variants.