This gene sequencing panel includes both sequencing and deletion/duplication (CNV) analysis for all coding regions of the included genes (unless otherwise noted). All analysis is performed utilizing next-generation sequencing (NGS) technology. All variants are classified according to American College of Genetics and Genomics (ACMG) guidelines.

Facioscapulohumeral muscular dystrophy (FSHD) is characterized by muscle weakness and wasting. This condition gets its name from the muscles that are affected most often: those of the face (facio-), around the shoulder blades (scapulo-), and in the upper arms (humeral). The signs and symptoms of FSHD usually appear in adolescence. However, the onset and severity of the condition vary widely. Milder cases may not become noticeable until later in life, whereas rare severe cases become apparent in infancy or early childhood. Weakness involving the facial muscles or shoulders is usually the first symptom of this condition. Facial muscle weakness often makes it difficult to drink from a straw, whistle, or turn up the corners of the mouth when smiling. Weakness in muscles around the eyes can prevent the eyes from closing fully while a person is asleep, which can lead to dry eyes and other eye problems. For unclear reasons, weakness may be more severe on one side of the face than the other. Weak shoulder muscles tend to make the shoulder blades protrude from the back, a common sign known as scapular winging. Weakness in the shoulders and upper arms muscles can make it challenging to raise the arms over the head or throw a ball. The muscle weakness associated with FSHD worsens slowly over decades and may spread to other body parts. Weakness in muscles of the lower legs can lead to a condition called foot drop, which affects walking and increases the risk of falls. Muscular weakness in the hips and pelvis can make climbing stairs or walking long distances difficult. Additionally, affected individuals may have an exaggerated lower back curvature (lordosis) due to weak abdominal muscles. About 20 percent of affected individuals eventually require the use of a wheelchair. Additional signs and symptoms of FSHD include mild high-tone hearing loss and retinal abnormalities. These signs are often not noticeable and may only be discovered during medical testing. FSHD rarely affects the heart or respiratory muscle. Researchers have described two types of FSHD: type 1 (FSHD1) and type 2 (FSHD2). Both types have the same signs and symptoms and are only distinguished by their genetic cause.

Sequencing is performed on genomic DNA using an Agilent targeted sequence capture method to enrich for the exome. Direct sequencing of the amplified captured regions was performed using 2X150bp 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. A list of these regions, if any, is available upon request. Alignment to the human reference genome (GRCh37) is performed and annotated variants are identified in the targeted region. Variants reviewed have a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Indel and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at director 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 detects deletions and duplications; in some instances, due to the size of the exons, sequence complexity, or other factors, not all CNVs may be analyzed or may be difficult to detect. When reported, copy number variant size is approximate. Actual breakpoint locations may lie outside of the targeted regions. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, and genomic imbalances in segmentally duplicated regions. 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 bcl2fastq converter v2.19. Secondary analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.10.8. Tertiary data analysis is performed using SnpEff v5.0 and Revvity Omics’ internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using BioDiscovery’s NxClinical v6.1 software.