Investigation of pathogenic variations by whole exome sequencing in familial amyotrophic lateral sclerosis cases excluding four major ALS genes

Objective: We aimed to identify using whole exome sequencing (WES) the genetic profiles of eight familial ALS cases in which conventional sequencing analysis revealed no genomic alterations in C9ORF72, SOD1, TARDBP and FUS genes, most commonly associated with Amyotrophic Lateral Sclerosis (ALS). Method: Rare ALS-associated variants consistent with the clinical phenotype of the patient were identified by WES analysis. Bioinformatics algorithms were used to determine the pathogenic effects of the variants on the proteins. The variants were validated by PCR-based Sanger sequencing in the index patient and his/her family members. Results: OPTN c.1400A>C: p.Gln467Pro and SPG11 c.6759C>G: p.Asp2253Glu gene variants with autosomal recessive inheritance were found in two of the families under investigation. In the remaining six cases, heterozygous genomic alterations in ALS-associated genes (dominant inheritance) were identified. Candidate variants in two different genes, KIF5A c.2738delG: p.Gly913AlafsTer135 and CAPN3 c.1469G>A: p.Arg490Gln were observed in the same patient. ANXA11 variants (c.1156C>T: p.Arg386Trp and c.1211G>A: p.Arg404Gln) were detected in two unrelated families. Variants in the FIG4 c.318T>G: p.Tyr106Ter, CYLD c.1189C>T: p.Arg397Cys and HSPB1 c.139G>A: p.Gly47Ser genes were detected in three independent cases. Conclusion: Homozygous variants in OPTN and SPG11 genes explained the phenotype in two patients with consanguineous parents. In one patient, a KIF5A gene variant was found to be responsible for ALS, while the effect of the pathogenic CAPN3 variant in the same patient, is subject for further research. Although the variants determined in the ANXA11 and HSPB1 genes cannot be considered the definite cause of ALS in the light of our current knowledge, clinical follow-up of asymptomatic individuals carrying the variant in the family through presymptomatic tests may be useful.