FSHD Type 2 Test

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 a targeted sequence capture method to enrich for the exome. Captured regions are sequenced on a short-read next-generation sequencing (NGS) system. Coverage requirements are based on validation data. An exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered. Alignment to the human reference genome is performed, and annotated variants within the targeted region are identified. Variants are reviewed based on minimum coverage and alternate allele frequency cutoffs defined as per laboratory procedure. Indel and single-nucleotide variants (SNVs) may be confirmed by Sanger sequencing analysis before reporting, based on laboratory requirements.

This assay cannot detect variants in regions that are not targeted, including deep intronic, promoter, or enhancer regions. Exons with nonunique sequences, such as those containing pseudogene regions, are not analyzed in this assay. Copy number variation (CNV) analysis detects deletions and duplications in genes on this panel; however, in some instances, due to exon size, sequence complexity, or other factors, certain CNVs may be difficult to detect and analyze. When reported, copy number variant size is approximate, and actual breakpoint locations may lie outside of the targeted regions. Only CNVs identified in genes included in the panel will be reported. This assay does not interrogate CNVs in mitochondrial DNA. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, or genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; however, possible cases of mosaicism may be detected and reported if laboratory requirements are met.

Primary data analysis is performed using standard FASTQ conversion tools appropriate to the sequencing platform. Secondary analysis is conducted using a high-performance genomic analysis pipeline. Tertiary analysis incorporates established annotation tools together with Revvity Omics' internal software. Copy number variation and absence of heterozygosity assessments are performed using a clinical cytogenomics platform.