Targeted next-generation sequencing reveals novel and rare variants in Indian patients with amyotrophic lateral sclerosis

Abstract

Studies on genetic aberrations among Indian amyotrophic lateral sclerosis (ALS) patients are limited to C9orf72 and ATXN2 repeat expansions and mutations in the SOD1 gene. In this study, we used targeted next-generation sequencing to analyze 25 ALS-associated genes in a cohort of 154 Indian ALS patients. We identified known pathogenic mutations in SOD1 (G148D; H44R), TARDBP (M337V; N267S), DAO (R199Q), and ANG (K41I). In addition, we also identified 7 potentially pathogenic missense variants that have not been previously reported in ALS patients; this includes 3 novel variants (OPTN: K489E, DAO: E121K, and SETX: L2163V) that are not reported in large population databases and 4 rare variants (CHMP2B: E45K, SQSTM1: G262R and P438L, ERBB4: R103H) with a minor allele frequency of <0.01 in large population databases. All known pathogenic, novel, and rare variants were detected in only 1 ALS patient each with the exception of the OPTN (K489E) variant that was detected in 2 patients in our cohort. In sum, we identified known and potentially pathogenic novel and rare mutations in 14 (9.1%) ALS patients in our cohort. This study represents the first comprehensive genetic analysis in the ethnically diverse population and thus provides a new insight into the genetics of Indian ALS patients.

Introduction

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by progressive degeneration of upper and lower motor neurons leading to progressive motor weakness and finally death due to respiratory failure within 3–5 years of symptom onset. Around 10% of ALS cases are categorized as familial based on family history, and 90% cases are sporadic. It is now clear that sporadic ALS (sALS) also has a strong genetic basis, and most familial ALS (fALS)-linked genes have been implicated in sALS either by de novo mutations or mutations which were earlier undetected due to incomplete penetrance, late onset of disease, and unavailability of patient material (Al-Chalabi and Lewis, 2011, Brown and Al-Chalabi, 2017).

Thus far, more than 120 genes have been reported to be associated with ALS (Abel et al., 2012), many of which have been observed repeatedly by different groups. Investigating the genetic basis of ALS has given researchers a better understanding of the causal mechanisms of neurodegeneration and has facilitated the development of disease models for testing targeted therapeutics (Al-Chalabi et al., 2013). The key genes associated with ALS manifestation include C9orf72, SOD1, TARDBP, FUS, OPTN, VCP, UBQLN2, and PFN1. Recently, novel/rare variants have been identified in ALS patients using next-generation sequencing (NGS) (Nakamura et al., 2016, Nishiyama et al., 2017).

Most previous studies on ALS genetics were conducted on populations of European ancestry. In the last few years, studies on genetic aberrations in ALS have been reported from various ethnic groups. Recent findings indicate a diverse genetic basis in ALS patients from different regions of the world (Renton et al., 2014) and that incidence of ALS is higher in whites as compared to that in African, Asian, and Hispanic ethnicities (Cronin et al., 2007). Reports on the genetic architecture of ALS in the Indian population are limited to C9orf72 and ATXN2 repeat expansions (Narain et al., 2017, Vats et al., 2017) and mutations in the SOD1 gene (Vats et al., 2016). Indians belong to diverse ethnic and racial groups, and a previous report demonstrates that Indian ALS patients exhibit a unique characteristic of extended life expectancy as compared to the western counterparts (Nalini et al., 2008), suggesting the existence of potentially novel genetic basis of ALS among Indian patients. The aim of our work is to explore the genetic basis of ALS in Indian patients.