Role of genetics in amyotrophic lateral sclerosis: a large cohort study in Chinese mainland population

Abstract

Background: A large number of new causative and risk genes for amyotrophic lateral sclerosis (ALS) have been identified mostly in patients of European ancestry. In contrast, we know relatively little regarding the genetics of ALS in other ethnic populations. This study aims to provide a comprehensive analysis of the genetics of ALS in an unprecedented large cohort of Chinese mainland population and correlate with the clinical features of rare variants carriers.

Methods: A total of 1587 patients, including 64 familial ALS (FALS) and 1523 sporadic ALS (SALS), and 1866 in-house controls were analysed by whole-exome sequencing and/or testing for G4C2 repeats in C9orf72. Forty-one ALS-associated genes were analysed.

Findings: 155 patients, including 26 (40.6%) FALS and 129 (8.5%) SALS, carrying rare pathogenic/likely pathogenic (P/LP) variants of ALS causative genes were identified. SOD1 was the most common mutated gene, followed by C9orf72, FUS, NEK1, TARDBP and TBK1. By burden analysis, rare variants in SOD1, FUS and TARDBP contributed to the collective risk for ALS (p<2.5e-6) at the gene level, but at the allelic level TARDBP p.Gly294Val and FUS p.Arg521Cys and p.Arg521His were the most important single variants causing ALS. Clinically, P/LP variants in TARDBP and C9orf72 were associated with poor prognosis, in FUS linked with younger age of onset, and C9orf72 repeats tended to affect cognition.

Conclusions: Our data provide essential information for understanding the genetic and clinical features of ALS in China and for optimal design of genetic testing and evaluation of disease prognosis.

Keywords: genetic variation; genetics; medical; neurodegenerative diseases.

Figure 1

Flow chart of the study. ACMG, American College of Medical Genetics; ALS, amyotrophic lateral sclerosis; BWA: Burrows-Wheeler Aligner; GATK: The Genome Analysis Toolkit; GI, group I, causative genes; GII, group II, new, needing to be confirmed or risk genes; GnomAD-EAS, Genome Aggregation Database-East Asian; IGV: Integrative Genomics Viewer; P/LP, pathogenic or likely pathogenic; RP-PCR, repeat-primed PCR; SKAT, sequencing kernel association test; VUS, variants of uncertain significance.

Figure 2

Regional distribution and genetic characteristics of patients with ALS in the study. (A) Distribution of patients with ALS in the study. Most of them came from Southwest China. (B) Type and proportion of rare variants identified in the study. (C) Mutation frequencies of each ALS causative gene in FALS and proportion of rare variants of each ALS causative gene in all the identified rare variants in FALS. (D) Mutation frequencies of each ALS causative gene in SALS and proportion of rare variants of each ALS causative gene in all the identified rare variants in SALS. ALS, amyotrophic lateral sclerosis; FALS, familial ALS; SALS, sporadic ALS; VUS, variants of uncertain significance.

Figure 3

Mutation spectrum according to age of onset in patients with ALS and the genotype and phenotype correlation in ALS causative genes. (A) Mutation frequencies of patients in different groups of age of onset. (B) Ranking of frequencies of rare P/LP variants in ALS causative genes in patients whose age of onset was less than 30 years (n=36, total patients; n=12, patients with P/LP variants), more than 30 years but less than 50 years (n=562, total patients; n=64, patients with P/LP variants), and more than 50 years (n=989, total patients; n=79, patients with P/LP variants). (C) Genotype and phenotype correlation of six most frequent mutated genes, including SOD1 (n=43), FUS (n=19), TARDBP (n=15), C9orf72 (n=20), TBK1 (n=10) and NEK1 (n=17). None means patients without rare variants of the GI genes (n=1376). The phenotype, including family history, sex ratio, initial spinal symptoms, cognitive functional impairment, frontal behaviour impairment, progression rate, age of onset and median survival time were analysed. For age of onset, it was 47.4±11.6 years in patients with SOD1 variants, 39.5±12.7 years in patients with FUS variants, 54.0±10.0 years in patients with TARDBP variants, 55.5±8.2 years in patients with C9orf72 G4C2 repeats, 49.0±16.5 years in patients with TBK1 variants, 57.5±10.8 years in patients with NEK1 variants and 54.2±11.4 years in patients without rare variants of the GI genes. Significant differences were found between patients with FUS variants and without rare variants of the GI genes (p=3.0E-8) and between patients with SOD1 variants and without rare variants of the GI genes (p=0.0001). For median survival time, it was 30.5 (95% CI 25.1 to 35.9) months in patients with SOD1 variants, 35.8 (95% CI 31.5 to 40.0) months in patients with FUS variants, 20.0 (95% CI 15.2 to 24.9) months in patients with TARDBP variants, 30.9 (95% CI 25.4 to 36.5) months in patients with C9orf72 G4C2 repeats, 26.9 (95% CI 16.8 to 37.0) months in patients with TBK1 variants, 60.5 (95% CI 25.0 to 95.9) months in patients with NEK1 variants and 42.6 (95% CI 40.0 to 45.3) months in patients without rare variants of the GI genes. Significant differences were found between patients with TARDBP variants and without rare variants of the GI genes (p=6.0E-5) and between patients with C9orf72 G4C2 repeats and without rare variants of the GI genes (p=0.012) (***p<0.001). (D) Clinical characteristics of rare special P/LP variants in ALS causative genes identified in more than one patient. ACER, Addenbrooke’s Cognitive Examination-Revised; ALS, amyotrophic lateral sclerosis; FAB, Frontal Assessment Battery; GI, group I; P/LP, pathogenic/likely pathogenic.

Figure 4

Comparison of initial symptoms, age of onset and median survival time among patients with rare P/LP variants in the GI genes (n=155), rare deleterious variants in the GII genes (n=100) and without rare damaging variants in the GI and GII genes (n=1276). (A) Ratio of patients presenting limb onset or bulbar onset (*p<0.05, **p<0.01). (B) The mean age of onset was 50.4±12.9 years in patients with rare P/LP variants in the GI genes, 55.8±12.0 years in patients with rare deleterious variants in the GII genes and 54.1±11.4 years in patients without rare damaging variants in the GI and GII genes. The mean age of onset in patients with rare P/LP variants in the GI genes was younger than that in patients with rare deleterious variants in the GII genes (***p<0.001) and in patients without rare damaging variants in the GI and GII genes (***p<0.001). (C) The median survival time was 34.0 (95% CI 28.4 to 39.6) months in patients with rare P/LP variants in the GI genes, 42.3 (95% CI 33.5 to 51.1) months in patients with rare deleterious variants in the GII genes and 42.6 (95% CI 39.9 to 45.3) months in patients without rare damaging variants in the GI and GII genes. Significant difference was found between patients with rare P/LP variants in the GI genes and without rare damaging variants in the GI and GII genes (p=0.011). GI, group I; GII, group II; P/LP, pathogenic/likely pathogenic.