Targeted resequencing identifies rare and novel sequence variants in Black South African and Nigerian Parkinson's disease patients

Background: Parkinson's disease (PD) is a common and debilitating neurological disorder with a significant genetic aetiology. Genetic factors have been well-studied in patients from North America, Europe and Asia but studies on other populations, particularly from the sub-Saharan African (SSA) region, have been limited. Here, we aimed to screen Black SSA PD patients for pathogenic mutations in genes known to be linked to PD as well as genes that have been associated with other neurological diseases and brain function. Methods: We recruited, with informed written consent, 33 Black South African and 14 Nigerian PD patients and screened them for mutations in 751 genes using a commercially-available Ion AmpliSeq™ Neurological Research panel. Massively parallel sequencing was performed on the Ion S5™ System using the Ion S5™ Sequencing Solutions and Sequencing Reagent Kits at the DNA Sequencing Unit, Central Analytical Facilities of Stellenbosch University, Stellenbosch, South Africa. bcftools was used to filter variants and we used a quality score >100 and a minimum read depth of >40. Annovar utility software was used for the annotation. We removed variants with minor allele frequency >0.01 in any of the frequency databases and used prediction scores for MetaLR and MetaSVM for selecting potentially deleterious sequence variants. Results. A total of 14,655 rare variants with a minor allele frequency =0.01 were identified in the 47 patients. Of these 7,934 were intronic, 5,695 exonic, 27 intergenic, 539 in untranslated regions, and 430 were in non-coding RNA. They included 3,175 synonymous and 2,448 missense variants. A total of 60 rare variants in 44 genes were selected and were considered to be deleterious on the basis of their MetaLR and MetaSVM scores. Of these, seven were in known PD genes ATP13A2, PRKN and PINK1. Some of the variants were shared by more than one patient but the significance of this finding is not known. Conclusions: Since none of the known mutations including the common G2019S in LRRK2 was found, we conclude that this group of patients may harbour novel mutations. Further follow-up studies are needed to investigate the functional significance of the rare variants identified, and their potential role in PD pathogenicity. This study illustrates the need for studies on diverse populations worldwide as genetic risk and protective factors for PD are likely to be ethnicity-specific, as has been shown for LRRK2