Who bears the burden? Rare-variant burden testing in sub-gene units to identify ALS hotspots

Abstract

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with a large genetic component. Many of the variants seen in ALS patients and controls are so rare that a potential association between the variant and ALS cannot be detected with genome-wide association studies (GWAS). Instead, rare-variant burden (RVB) tests can be used, which combine the signal of all variants in a gene into one signal. A potential limitation of this technique is that the signal of a group of damaging variants can be weakened by the presence of neutral or protective variants in the same gene. Because damaging mutations might occur in different densities across the gene, this research aims to reduce the limitation of testing neutral and damaging mutations together by using two different methods of grouping variants: a functional domain-based method and a spatial clustering method based on the distances between variants. Both methods were tested on three ALS-associated genes: SOD1, FUS and NEK1. The patterns of damaging mutations found in previous studies of SOD1 and FUS were replicated, i.e. no hotspots were seen in SOD1, while robust hotspots of rare and ultra-rare variants were seen in the C-terminus of FUS. In NEK1, two clusters dependent on single intermediate-frequency variants were seen. Additionally, an enrichment of damaging rare variants was found at the N-terminus of NEK1. While the spatial clustering method resulted in more consistent hotspots of ALS variants than the functional-domain based methods, combining both methods strengthens the evidence for hotspots and facilitates the interpretation of the significant results. All in all, this method has the potential to find new hotspots in known ALS genes or new genes that are associated with ALS.