Facioscapulohumeral Muscular Dystrophy Type 2 (FSHD2) NGS Panel

Clinical Information

Facioscapulohumeral muscular dystrophy (FSHD) is a highly variable disorder characterized by progressive and often asymmetric muscle weakness in the face, scapular stabilizers, shoulders, arms, lower legs, and hip girdle. Two types of FSHD have been described: FSHD1 and FSHD2.

FSHD1 is the most common form and is observed in >95% of individuals diagnosed with FSHD, whereas FSHD2 is observed in the remaining <5% of cases. Both FSHD1 and FSHD2 are caused by abnormal epigenetic activation of the DUX4 gene, a transcription factor that is normally silenced. DUX4 is either encoded with a polyadenylation sequence (termed the 4qA permissive haplotype) or without a polyadenylation sequence (4qB non-permissive haplotype). Contraction of the D4Z4 repeat array on the permissive 4qA haplotype is consistent with a diagnosis of, or a predisposition to develop FSHD1. In FSHD2, hypomethylation of the D4Z4 repeat array can be the result of a heterozygous pathogenic variant in SMCHD1 or DNMT3B, or biallelic pathogenic variants in LRIF1, in the presence of a 4qA permissive allele.

Technical Information

This panel is performed by Next Generation Sequencing and covers the coding regions of the listed genes and the flanking intronic sequences. Promoter, 3′ untranslated sequences, and deep intronic sequences are also covered, but only known disease-causing variants in these regions will be reported. Variants identified on the panel are confirmed with Sanger sequencing if they do not meet certain quality thresholds.

Large deletions and duplications (CNVs) affecting the genes of the panel can be detected; however, due to defined settings in the analysis software, CNVs smaller than 2-kb may not be identified (for example, some small exonic level copy number changes may not be identified). Please note that certain types of genetic alterations including trinucleotide repeat expansions, methylation abnormalities, and balanced rearrangements (e.g., inversions, reciprocal translocations) may not be detected by the current analysis.

Specimen Requirements

• The preferred sample type is 3-4 ml of peripheral blood collected in an EDTA (purple top) tube. Extracted DNA and saliva are also accepted for this test. Blood and saliva kits are available by request.
• Send approximately 5µg of extracted DNA at a requested concentration of 90-130 ng/µl.
• If saliva is submitted, and the extracted DNA is below quality control, then you will be contacted to submit a blood sample or the panel can be completed on an exome backbone. Saliva samples must be submitted in an approved saliva kit.

Transport Instructions

• The blood specimen should be kept at room temperature and delivered via overnight shipping. If shipment is delayed by one or two days, the specimen should be refrigerated and shipped at room temperature. Do not freeze the specimen. Samples collected on Friday can be safely designated for Monday delivery.
• Extracted DNA should be sent at room temperature via overnight delivery.
• Saliva is stable at room temperature and can be delivered via overnight or ground shipping.