Tackling Neurodegeneration Using Next-generation Sequencing: Identifying the Genetics of Five Neurodegenerative Disorders

Farhan, SMK., Liang, E., McIntyre, AD., Cao, H., Robinson, JF., Volkening, K., Bulman, DE., Rogaeva, E., St. George-Hyslop, P., Masellis, M., Strong, MJ., and Hegele, RA., for the ONDRI Investigators

Our group is a part of the Ontario Neurodegeneration Disease Research Initiative (ONDRI), a program aiming to characterize five neurodegenerative disorders namely, 1) amyotrophic lateral sclerosis (ALS); 2) frontotemporal dementia; 3) Alzheimer’s disease; 4) Parkinson’s disease; and 5) vascular cognitive impairment (VCI). We are focusing on identifying the genetic determinants of these five neurodegenerative disorders, which can provide insight into new molecular pathways and may have broader implications for diagnosis and treatment. We hypothesize the five neurodegenerative disorders under study are complex genetic diseases partly caused by rare, pathogenic single mutations or multiple, low-effect mutations acting synergistically to mediate disease expression. As next-generation sequencing (NGS) allows for efficient genetic variant detection, we have engineered a NGS based custom-designed resequencing gene panel that allows us to screen patients for mutations in 80 genes known to be implicated in neurodegenerative disease pathways. We plan to use the gene panel termed ‘ONDRISeq’, to sequence DNA collected from >600 patients across all five neurodegenerative diseases to identify genetic variants contributing to disease expression. To determine if the newly found genetic variants are disease causing, the NGS data will be filtered through a non-synonymous, rare variant prioritization analysis. These variants will be further annotated based on the location and the type of mutation they introduce. We plan to use multiple bioinformatics programs to predict the consequence on the protein function exerted by the mutations; and more importantly, the overall carrier frequency of these mutations. Furthermore, in some cases where there is a family history of the disease, we plan to sequence their relatives to determine whether the genetic variants co-segregate with disease status in a specific inheritance pattern. Finally, we plan to study some of the genetic variants in biological systems to recapitulate aspects of the human disorder providing further evidence for gene based disease expression. To date, ONDRISeq is the first, proprietary gene panel able to process a multitude of neurodegenerative diseases. However, analysis of 80 genes can yield an excess of genetic variation, which needs to be processed to discriminate between clinically-relevant variants from those of uncertain significance. The 600 patients are clinically heterogeneous, with some patients presenting with a single, discrete disease while others present with multiple features from ≥2 different diseases. This discordance in presentation may be explained by genetic variation. Patients presenting with a spectrum of phenotypes such as ALS and dementia are likely carrying multiple mutations found in multiple disease genes. With the approaching tidal wave of patients affected by neurodegeneration, a thorough understanding of primary genetic causes using DNA sequencing promises to generate faster diagnosis, better prognosis, and successful gene therapies. Our application of NGS in complex, multifactorial disorders has the potential to identify disease- specific risk markers and potentially, overlapping pathways common in all five diseases.