Hereditary Dementia and Amyotrophic Lateral Sclerosis Panel

ALS is a progressive condition that affects motor neurons. In ALS, motor neurons die over time, leading to muscle weakness, a loss of muscle mass, and an inability to control movement. There are different types of ALS, distinguished by their signs and symptoms and their genetic cause or lack of clear genetic association. Approximately 5,000 people in the United States are diagnosed with ALS each year. Mutations in several genes can cause familial ALS. The C9orf72 repeat expansion accounts for 30-40% of familial ALS. The SOD1 gene causes 15-20% of familial ALS, and then TARDBP and FUS gene mutations make up approximately 5% of familial cases.

Sequencing is performed on genomic DNA using an Agilent targeted sequence capture method to enrich for the genes on this panel. Direct sequencing of the amplified captured regions was performed using 2X100bp reads on Illumina next-generation sequencing (NGS) systems. A base is considered to have sufficient coverage at 20X and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. Low coverage regions, if any, are limited to ~1% or less of the nucleotides in the test unless a pathogenic variant explaining the phenotype is discovered. A list of these regions is available upon request. Alignment to the human reference genome (hg19) is performed and annotated variants are identified in the targeted region. Variants are called at a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Single nucleotide variants (SNVs) meeting internal quality assessment guidelines are confirmed by Sanger sequence analysis for records after results are reported. Indels and SNVs are confirmed by Sanger sequence analysis before reporting at the director's discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter, and enhancer regions, areas containing large numbers of tandem repeats, and variants in mitochondrial DNA. Copy number variation (CNV) analysis is designed to detect deletions and duplications of three exons or more; in some instances, due to the size of the exons or other factors, not all CNVs may be analyzed. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.4.12. Secondary and tertiary data analysis is performed using PerkinElmer’s internal ODIN v.1.01 software for SNVs and Biodiscovery’s NxClinical v.6.1 or Illumina DRAGEN Bio-IT Platform v.3.4.12 for CNV and absence of heterozygosity (AOH). Genes and/or exons located in pseudogene regions are not covered in this assay.