Exome array analysis of rare and low frequency variants in amyotrophic lateral sclerosis

Abstract

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that affects 1 in ~350 individuals. Genetic association studies have established ALS as a multifactorial disease with heritability estimated at ~61%, and recent studies show a prominent role for rare variation in its genetic architecture. To identify rare variants associated with disease onset we performed exome array genotyping in 4,244 cases and 3,106 controls from European cohorts. In this largest exome-wide study of rare variants in ALS to date, we performed single-variant association testing, gene-based burden, and exome-wide individual set-unique burden (ISUB) testing to identify single or aggregated rare variation that modifies disease risk. In single-variant testing no variants reached exome-wide significance, likely due to limited statistical power. Gene-based burden testing of rare non-synonymous and loss-of-function variants showed NEK1 as the top associated gene. ISUB analysis did not show an increased exome-wide burden of deleterious variants in patients, possibly suggesting a more region-specific role for rare variation. Complete summary statistics are released publicly. This study did not implicate new risk loci, emphasizing the immediate need for future large-scale collaborations in ALS that will expand available sample sizes, increase genome coverage, and improve our ability to detect rare variants associated to ALS.

Figure 1

Quantile-quantile plot and Manhattan plot of p-values of the single-variant association analysis. (A) Quantile-quantile plot of single-variant association analysis using logistic regression binned by minor allele frequency. (B) Manhattan plot of p-values of exome-wide association testing comprising 7350 individuals (4,244 cases and 3,106 controls) and 100,896 non-monomorphic variants. The x axis depicts chromosomal position and the y axis shows the significance of association derived by logistic regression. The dotted line corresponds to the exome-wide significance threshold of p = 5 × 10⁻⁷).

Figure 2

Gene mutation plot of NEK1. The orange circles represent exons relative to their size in basepairs. The vertical lines represent the distribution of SNVs across NEK1 in the gene-based test (SKAT-O), with their corresponding amino acid change, minor allele frequency (MAF) and odds ratio (OR) in the single-variant analysis.