Enrichment of Rare Protein Truncating Variants in Patients with Amyotrophic Lateral Sclerosis

Sali M.K. Farhan, Daniel P. Howrigan, Liam E. Abbott, Andrea E. Byrnes, Claire Churchhouse, FALS Consortium, ALSGEN Consortium, Mark J. Daly, and Benjamin M. Neale

Analytic and Translational Genetics Unit, Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard

Amyotrophic lateral sclerosis (ALS) is a genetically and phenotypically heterogeneous neurodegenerative disease. Genetic variation is an important risk factor for ALS. Given that 5- 10% of patients reporting a positive family history and ~10% of sporadic patients carrying known familial ALS gene mutations, the distinction between familial and sporadic disease is increasingly blurred. To discover novel genetic risk factors underlying ALS, we aggregated exomes from 3,864 cases and 7,839 ancestry matched controls, the largest ALS exome-based case-control study to date. We complemented our analysis by leveraging allele frequencies from large external exome sequencing databases such as DiscovEHR (>50,000 samples) and the non- brain related subset of ExAC (>45,000 samples). We observed a significant excess of ultra-rare and rare protein-truncating variants (PTV) among ALS cases, which was primarily concentrated in genes recognizably intolerant of truncating mutation (constrained genes); however, a significant enrichment in PTVs does persist in the remaining exome. There was no enrichment of rare PTVs in genes known to confer risk to ALS; genes associated with clinically overlapping diseases; or genes in which their expression is specific to the brain. We conducted gene level analyses, which highlighted three known ALS genes, SOD1, NEK1, and FUS, as the most strongly associated. We also observe suggestive statistical evidence for multiple novel genes including DNAJC7, which is a highly constrained gene, and a member of the heat shock protein family (HSP40). HSP40 proteins, along with HSP70 proteins, facilitate protein maintenance and quality control, such as folding of newly synthesized polypeptides, and clearance of degraded proteins. When these processes are not regulated, misfolding and accumulation of degraded proteins can occur leading to aberrant protein aggregation, one of the pathological hallmarks of neurodegenerative diseases.