Clinical Utility of Whole-Genome Sequencing in an ALS Cohort
Adriano Chio1, Andrea Calvo2, Cristina Moglia3, Maura Brunetti4, Ruth Chia6, Jinhui Ding6, J. Raphael Gibbs6, Clifton Dalgard7, Sonja Scholz8, Bryan Traynor9, Letizia Mazzini10, Fabiola De Marchi10, Lucia Corrado11, Sandra D'Alfonso11, Maurizio Grassano5
1Department of Neuroscince, University of Torino, 2Dept. of Neuroscience, University of Turin, Italy, 3University of Torino, 4Neuroscience, University of Turin, 5University of Turin, 6NIH, NIA, 7Uniformed Services University of the Health Sciences, 8National Institute of Neurological Disorders and Stroke, 9National Institute on Aging, 10University of Novara, 11University of Eastern Piedmont
Objective:

To provide a comprehensive analysis of frequency and spectrum of known genetic risk in ALS patients and assess the clinical utility of performing next-generation sequencing.

Background:

The complex genetic landscape in ALS presents a significant challenge in the clinical setting. Despite the increasing number of pathogenic/risk mutations reported in ALS, the true proportion of cases that can be attributed to genetic factors remains unclear and the actual role of genome-wide screening in clinical practice is still undetermined.

Design/Methods:

Whole-exome sequencing was performed on 950 ALS cases and 675 control samples from an Italian population-based ALS cohort. We screened for coding single-nucleotide variants, indels and expansion in 60 ALS-related genes. Variants were classified by likelihood of pathogenicity according to a pipeline that accounted for minor allele frequency, absence from the control cohort and integrated pathogenicity predictions. Samples were also screened for known repeated expansions.

Results:

We identified 21 pathogenic and likely pathogenic variants, 29 loss of function variants and 180 missense variants classified as deleterious according to our pipeline. These variants were observed in 191 patients (20.1% of our cohort). 71 patients (7.5%) carried the C9ORF72 hexanucleotide expansion.

Overall, 24.7% of our cohort carried a pathogenic mutation and 3% of cases were found to carry multiple pathogenic variants. Furthermore, we observed the ATXN2 intermediate repeat in 36 patients (3.8%). Age at onset (p<0.0252) and family history (p< 0.00001) predicted the likelihood of finding a genetic factor, while gender, site of onset and clinical picture did not.

Conclusions:

We conclusively show that genetic mutations and risk factors in both familial and sporadic ALS patients are more common than previously thought, thus highlighting that genetics play a central role in ALS pathogenesis. Next-generation genetic testing should be offered to all patients diagnosed with ALS for both diagnostic and prognostic purposes.