High-Throughput Genetic Testing in ALS: The Challenging Path of Variant Classification Considering the ACMG Guidelines

• Published in: Genes 2020-10, Vol.11 (10), p.1123
• Main Authors: Lattante, Serena, Marangi, Giuseppe, Doronzio, Paolo Niccolò, Conte, Amelia, Bisogni, Giulia, Zollino, Marcella, Sabatelli, Mario
• Format: Article
• Language: English
• Subjects: Amyotrophic lateral sclerosis; Classification; Diagnosis; Gene frequency; Genes; Genetic aspects; Genetic counseling; Genetic diversity; Genetic screening; Genetic testing; Genomes; Genomics; High-throughput screening (Biochemical assaying); Methods; Next-generation sequencing; Patients; Polygenic inheritance; Population; Practice guidelines (Medicine); Risk factors; Software
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes11101123

The development of high-throughput sequencing technologies and screening of big patient cohorts with familial and sporadic amyotrophic lateral sclerosis (ALS) led to the identification of a significant number of genetic variants, which are sometimes difficult to interpret. The American College of Medical Genetics and Genomics (ACMG) provided guidelines to help molecular geneticists and pathologists to interpret variants found in laboratory testing. We assessed the application of the ACMG criteria to ALS-related variants, combining data from literature with our experience. We analyzed a cohort of 498 ALS patients using massive parallel sequencing of ALS-associated genes and identified 280 variants with a minor allele frequency < 1%. Examining all variants using the ACMG criteria, thus considering the type of variant, inheritance, familial segregation, and possible functional studies, we classified 20 variants as “pathogenic”. In conclusion, ALS’s genetic complexity, such as oligogenic inheritance, presence of genes acting as risk factors, and reduced penetrance, needs to be considered when interpreting variants. The goal of this work is to provide helpful suggestions to geneticists and clinicians dealing with ALS.