Novel and rare variants in amyotrophic lateral sclerosis genes identified in Malaysian patients

There is limited information on the genetic architecture of amyotrophic lateral sclerosis (ALS) in Southeast Asian populations. To address this knowledge gap, we performed 1) SOD1 (exon 1-4), FUS (exon 13-15), TARDBP (exon 6) and ATXN2 repeat expansion screening in 201 multi-ethnic Malaysian (Malay, Chinese, Indian and others) ALS patients, 2) C9orf72 repeat expansion testing in 179 subset patients, and 3) a panel of 61 ALS-associated genes screening in 112 subset cases using either whole genome (n = 21) or exome (n = 91) sequencing datasets. Among the patients, the observed mutational frequencies in key ALS genes were: SOD1 3.0% (6/201), C9orf72 2.2% (4/179), ATXN2 2.0% (4/201), FUS 1.5% (3/201), and TARDBP 1.5% (3/201). Of the 112 cases that underwent WGS/WES, 6.3% (7/112) comprised of pathogenic and likely pathogenic variants in FIG4 (p.Lys657Serfs*2), FUS (p.Arg485Profs*32), TARDBP (p.Ile383del), NEK1 (p.Ile633Asnfs*28), GRN (c.599-1G > C), CYP27A1 (p.Met1Thr) and SPAST (p.Glu449Gly). Additionally, 42.9% (48/112) had at least one variant of uncertain significance (VUS) in 34 genes. Notably, in the 24 genes classified as 'definitive' by the ClinGen ALS Spectrum Disorders Gene Curation Expert Panel, five patients (4.5%, 5/112) harbored more than one likely pathogenic variant and/or VUS. However, burden analysis revealed no significant differences in clinical characteristics between patients with varying numbers of variants. Our findings highlight the utility of next-generation sequencing in elucidating the genetic basis of ALS in Malaysian and Southeast Asian ethnic groups, including the identification of several novel variants of clinical interest as well as increasing diagnostic yield up to 47.7%.