Oligogenic structure of amyotrophic lateral sclerosis has genetic testing, counselling and therapeutic implications

Abstract

Background: Despite several studies suggesting a potential oligogenic risk model in amyotrophic lateral sclerosis (ALS), case-control statistical evidence implicating oligogenicity with disease risk or clinical outcomes is limited. Considering its direct clinical and therapeutic implications, we aim to perform a large-scale robust investigation of oligogenicity in ALS risk and in the disease clinical course.

Methods: We leveraged Project MinE genome sequencing datasets (6711 cases and 2391 controls) to identify associations between oligogenicity in known ALS genes and disease risk, as well as clinical outcomes.

Results: In both the discovery and replication cohorts, we observed that the risk imparted from carrying multiple ALS rare variants was significantly greater than the risk associated with carrying only a single rare variant, both in the presence and absence of variants in the most well-established ALS genes. However, in contrast to risk, the relationships between oligogenicity and ALS clinical outcomes, such as age of onset and survival, did not follow the same pattern.

Conclusions: Our findings represent the first large-scale, case-control assessment of oligogenicity in ALS and show that oligogenic events involving known ALS risk genes are relevant for disease risk in ~6% of ALS but not necessarily for disease onset and survival. This must be considered in genetic counselling and testing by ensuring to use comprehensive gene panels even when a pathogenic variant has already been identified. Moreover, in the age of stratified medication and gene therapy, it supports the need for a complete genetic profile for the correct choice of therapy in all ALS patients.

Keywords: ALS; GENETICS; MOTOR NEURON DISEASE.

Figure 1. Singleton and oligogenic enrichment of rare variants (MAF < 0.01) in known ALS genes in individuals with ALS compared to controls. Enrichment of carriers of rare variants in one known ALS gene and carriers of rare variants in two or more known ALS genes was compared to non-carriers in individuals with ALS compared to controls. Enrichment analyses were performed using logistic regression in the discovery subset (individuals with ALS = 4299, controls = 1815) of the Project MinE ALS sequencing consortium dataset, including sex, 10 ancestry defining principal components, and total variant count (total genetic load) as covariates. The upset plot on the left legend indicates the variant types that the singleton or oligogenic variant may encompass; for example, the bottom row indicates the singleton variant or two or more oligogenic variants may be a C9orf72 repeat expansion, ATXN2 repeat expansion, missense variants, or protein truncating variants (PTVs). Synonymous variants, missense variants, and PTVs were identified in 24 known ALS genes using whole genome sequencing. ATXN2 and C9orf72 refer to a pathogenic repeat expansion being identified in the respective gene using ExpansionHunter. Minor allele frequencies were obtained from the GnomAD v2.1.1 non-neurological dataset. Abbreviations: CI, confidence interval; MAF, minor allele frequency; PTV, protein truncating variant.

Figure 2. Influence of singleton and oligogenic enrichment of rare variants (MAF < 0.01) in known ALS genes to ALS age of onset. The influence of carrying a rare variant in a single known ALS genes was compared to the influence of carrying rare variants in two or more known ALS genes on ALS age of onset in the discovery cohort of the Project MinE ALS sequencing consortium (individuals with ALS = 4299). Enrichment analyses were performed using linear regression including sex, site of onset, 10 ancestry defining principal components, and total variant count (total genetic load) as covariates. The upset plot on the left legend indicates the variant types that the singleton or oligogenic variant may encompass; for example, the bottom row indicates the singleton variant or two or more oligogenic variants may be a C9orf72 repeat expansion, ATXN2 repeat expansion, missense variants, or protein truncating variants (PTVs). Synonymous variants, missense variants, and PTVs were identified in 24 known ALS genes using whole genome sequencing. ATXN2 and C9orf72 refer to a pathogenic repeat expansion being identified in the respective gene using ExpansionHunter. Minor allele frequencies were obtained from the GnomAD v2.1.1 non-neurological dataset. Abbreviations: CI, confidence interval; MAF, minor allele frequency; PTV, protein truncating variant.

Figure 3. Influence of singleton and oligogenic enrichment of rare variants (MAF < 0.01) in known ALS genes to ALS survival period. The influence of carrying a rare variant in a single known ALS gene was compared to the influence of carrying rare variants in two or more known ALS genes on ALS survival period in the discovery cohort of the Project MinE ALS sequencing consortium (individuals with ALS = 4299). Enrichment analyses were performed using Cox proportional-hazards models including sex, site of onset, 10 ancestry defining principal components, and total variant count (total genetic load) as covariates. The upset plot on the left legend indicates the variant types that the singleton or oligogenic variant may encompass; for example, the bottom row indicates the singleton variant or two or more oligogenic variants may be a C9orf72 repeat expansion, ATXN2 repeat expansion, missense variants, or protein truncating variants (PTVs). Synonymous variants, missense variants, and PTVs were identified in 24 known ALS genes using whole genome sequencing. ATXN2 and C9orf72 refer to a pathogenic repeat expansion being identified in the respective gene using ExpansionHunter. Minor allele frequencies were obtained from the GnomAD v2.1.1 non-neurological dataset. Survival period was defined as years from diagnosis to death, or years from diagnosis to last follow-up, as appropriate. Abbreviations: CI, confidence interval; MAF, minor allele frequency; PTV, protein truncating variant.

Figure 4. Individuals with ALS carrying two or more rare variants in ALS genes. ALS, amyotrophic lateral sclerosis. (A) The number of individuals with ALS from the Project MinE discovery cohort (n = 4299) carrying at least one rare variant in each gene encompassed in the respective column and row. (B) The number of individuals with ALS from the Project MinE discovery cohort carrying at least one rare variant in an established ALS gene encompassed in the respective column and row. (C) The number of individuals with ALS from the Project MinE discovery cohort carrying at least one primary rare variant in an established ALS gene encompassed in the respective column and at least one secondary rare variant in a known ALS gene in the respective row. Established ALS genes were defined as those with a definitive ALS gene-disease relationship based on review by the ClinGen ALS Gene Curation Expert Panel. All remaining genes assessed were considered ALS-associated genes.