Mutational Analysis of Known ALS Genes in an Italian Population-Based Cohort

Abstract

Objective: To assess the burden of rare genetic variants and to estimate the contribution of known amyotrophic lateral sclerosis (ALS) genes in an Italian population-based cohort, we performed whole genome sequencing in 959 patients with ALS and 677 matched healthy controls.

Methods: We performed genome sequencing in a population-based cohort (Piemonte and Valle d'Aosta Registry for ALS [PARALS]). A panel of 40 ALS genes was analyzed to identify potential disease-causing genetic variants and to evaluate the gene-wide burden of rare variants among our population.

Results: A total of 959 patients with ALS were compared with 677 healthy controls from the same geographical area. Gene-wide association tests demonstrated a strong association with SOD1, whose rare variants are the second most common cause of disease after C9orf72 expansion. A lower signal was observed for TARDBP, proving that its effect on our cohort is driven by a few known causal variants. We detected rare variants in other known ALS genes that did not surpass statistical significance in gene-wise tests, thus highlighting that their contribution to disease risk in our cohort is limited.

Conclusions: We identified potential disease-causing variants in 11.9% of our patients. We identified the genes most frequently involved in our cohort and confirmed the contribution of rare variants in disease risk. Our results provide further insight into the pathologic mechanism of the disease and demonstrate the importance of genome-wide sequencing as a diagnostic tool.

Figure 1. Experimental Workflow

ACMG/AMP = American College of Medical Genetics and Genomics/Association for Molecular Pathology; ALS = amyotrophic lateral sclerosis; CMC = Combined-Multivariate Collapsing Burden Test; KBAC = Kernel-Based Adaptive Clustering Model; MAF = minor allele frequency; SKAT = Sequence-Based Kernel Association Test.

Figure 2. Frequency of Major Amyotrophic Lateral Sclerosis (ALS) Gene Mutations in our Cohort

(A) Relative contributions of ALS genes to the total estimate of patients harboring a causative variant. (B) Distribution of pathogenic variants among patients with sporadic ALS (sALS) and patients with ALS with a family history of the disease (fALS).

Figure 3. Results of Rare Variant Association Testing

Results of rare variant association testing with minor allele frequency (MAF) <5% (A) and <1% (B). Solid line: p value 0.05. Dashed line: Bonferroni-adjusted p value 0.001. All the log p values obtained by the gene-wise association tests applied in our study are reported. CMC = Combined-Multivariate Collapsing Burden Test; Fp = burden test with rare variants upweighted using frequency controls; Kbac = kernel-based adaptive clustering model; Madsen-Browning = Madsen-Browning Burden Test with rare variants upweighted using inverse frequency controls; Skat = Sequence-Based Kernel Association Test; SkatO = Optimized Sequence-Based Kernel Association Test; Zeggini = Zeggini-Morris Burden Test with aggregate counts of rare variants.