Value of systematic genetic screening of patients with amyotrophic lateral sclerosis

Abstract

Objective: The clinical utility of routine genetic sequencing in amyotrophic lateral sclerosis (ALS) is uncertain. Our aim was to determine whether routine targeted sequencing of 44 ALS-relevant genes would have a significant impact on disease subclassification and clinical care.

Methods: We performed targeted sequencing of a 44-gene panel in a prospective case series of 100 patients with ALS recruited consecutively from the Sheffield Motor Neuron Disorders Clinic, UK. All participants were diagnosed with ALS by a specialist Consultant Neurologist. 7/100 patients had familial ALS, but the majority were apparently sporadic cases.

Results: 21% of patients with ALS carried a confirmed pathogenic or likely pathogenic mutation, of whom 93% had no family history of ALS. 15% met the inclusion criteria for a current ALS genetic-therapy trial. 5/21 patients with a pathogenic mutation had an additional variant of uncertain significance (VUS). An additional 21% of patients with ALS carried a VUS in an ALS-associated gene. Overall, 13% of patients carried more than one genetic variant (pathogenic or VUS). Patients with ALS carrying two variants developed disease at a significantly earlier age compared with patients with a single variant (median age of onset=56 vs 60 years, p=0.0074).

Conclusions: Routine screening for ALS-associated pathogenic mutations in a specialised ALS referral clinic will impact clinical care in 21% of cases. An additional 21% of patients have variants in the ALS gene panel currently of unconfirmed significance after removing non-specific or predicted benign variants. Overall, variants within known ALS-linked genes are of potential clinical importance in 42% of patients.

Figure 1

Clinical screening of all patients with ALS identifies pathogenic, likely pathogenic and variants of uncertain significance (VUS). (A) The 44 genes covered by the clinical ALS panel (42 profiled by next-generation sequencing and 2 by PCR). Those genes in which pathogenic (red), likely pathogenic variants (orange) or VUS (blue) were identified after filtering. No pathogenic variants or VUS were found in the genes depicted in the white boxes. Background colour of the box represents the most severe variant found in that gene. (B) Schematic of our variant analysis and filtering process. (C) Counts of reportable (red) and variants of unknown significance in ALS genes in the Sheffield AMBRoSIA cohort. (D) Five clinically reportable variants in SOD1. (E) 4 Variants of unknown significance were discovered in SPG11. Interestingly, 3 of these cluster in the C-terminal domain. Benign and likely benign mutations are conversely distributed throughout the protein. Protein domain figures created using ProteinPaint (https://pecan.stjude.cloud/proteinpaint).

Figure 2

Increased mutation burden is associated with earlier age at onset. (A) Details of patients with two or more pathogenic, likely pathogenic or variants of uncertain significance (VUS) (n=13). (B) The number of pathogenic, likely pathogenic and VUS in each patient in the study. (C) Cumulative event plot showing those patients with two or more pathogenic, likely pathogenic or VUS have a significantly earlier age of onset.