Congenital Muscular Dystrophy (CMD) Panel

The congenital muscular dystrophies are a clinically and genetically heterogeneous group of disorders characterized by elevated serum CK levels, muscle weakness, a dystrophic process observed in biopsied muscle, and variable associated findings such as central nervous system abnormalities, cardiac muscle involvement, skeletal effects, and developmental delay (Bertini et al. 2011). Onset of symptoms generally occurs at birth, although some symptoms do not manifest until later in life. This panel includes testing for Merosin-deficient congenital muscular dystrophy, dystroglycanopathies including Walker-Warburg syndrome (WWS), Ullrich congenital muscular dystrophy, Bethlem myopathy, dystrophinopathies, Emery-Dreifuss muscular dystrophy, LMNA-related muscular dystrophies, and other rare forms of muscular dystrophy.

Congenital muscular dystrophies caused by pathogenic variants in LAMA2, CHKB, ITGA7, B3GALNT2 , B4GAT1, CRPPA/ISPD, DAG1 , DPM1, DPM2, DPM3, FKRP, FKTN, GMPPB, LARGE1, POMGNT1, POMGNT2, POMK, POMT1, POMT2, and RXYLT1/TMEM5 are inherited in an autosomal recessive manner. Pathogenic variants in these genes include missense, nonsense, splicing, and small deletions/insertions (http://www.dmd.nl/; Human Gene Mutation Database). Gross deletions/duplications have been commonly reported in the CRPPA/ISPD, LAMA2, and LARGE1 genes (Human Gene Mutation Database). LMNA related congenital muscular dystrophy is inherited as autosomal dominant disorder and many times occurs as a result of de novo mutation.

DMD and EMD both cause X-linked recessive muscular dystrophies. Approximately two-thirds of the pathogenic variants in Duchenne muscular dystrophy patients are deletions of one or more exons in the DMD gene. The occurrence of deletions is slightly higher in Becker muscular dystrophy patients. Duplications are found in approximately 10% of Duchenne muscular dystrophy patients and 20% of Becker muscular dystrophy patients. Pathogenic variants detectable by sequence analysis are found in approximately one-third of Duchenne muscular dystrophy cases and in approximately 20% of Becker muscular dystrophy cases. Emery-Dreifuss muscular dystrophy is caused by pathogenic variants in the EMD gene which include missense, nonsense, and splicing variants and also small out-of-frame insertions/deletions and gross deletions (Human Gene Mutation Database).

Most cases of Bethlem myopathy have autosomal dominant inheritance of COL6A1, COL6A2 or COL6A3 pathogenic variants (Lampe and Bushby 2005; Jobsis et al. 1999; Butterfield et al. 2013). Once thought to be strictly a recessive condition, Ullrich congenital muscular dystrophy has been shown to be inherited in a dominant manner in numerous cases (Pan et al. 2003). A dominant-negative effect underlies pathogenicity of dominantly inherited UCMD (Pan et al. 2003; Baker et al. 2005), while most cases of recessive UCMD result from truncating pathogenic variants. Recently, both dominant and recessive pathogenic variants in a fourth collagen gene, COL12A1, have been found in patients with Ullrich and Bethlem phenotypes (Hicks et al. 2014; Zou et al. 2014).

Because of extensive phenotypic and locus heterogeneity for the congenital muscular dystrophies, over-all clinical sensitivity is difficult to estimate. Based on results from both the literature and PreventionGenetics, we estimate that this test will detect pathogenic variants in roughly 45% of patients (Sparks et al. 2012). Pathogenic variants in LAMA2, which cause merosin-deficient CMD, are over-all the most common subtype of CMD. In one study (Allamad et al. 2002) merosin-deficient CMD was found to account for about 30% of the CMD cases in Europe. In a cohort of ninety fetuses with severe cobblestone lissencephaly and associated findings consistent with Walker-Warburg syndrome, Vuillaumier-Barrot et al (2012), found a genetic diagnosis in 58, or 64%. These diagnosed cases had relative frequencies as follows: POMT1 (42%), POMT2 (17%), POMGNT1 (17%), CRPPA/ISPD (9%), RXYLT1/TMEM5 (9%), LARGE1 (3%) and FKRP (3%). Sequence analysis using genomic DNA from peripheral blood was found to have clinical sensitivity of 66%, 56%, and 79% among patients classified as having typical Bethlem Myopathy, severe Bethlem Myopathy, and Ulrich Congenital Muscular Dystrophy, respectively (Lampe et al. 2005).

Clinical sensitivity of deletion/duplication testing for most of the CMD genes is low, except for the CRPPA/ISPD, DMD, LAMA2 and LARGE1 genes (Human Gene Mutation Database). Approximately two-thirds of the pathogenic variants in Duchenne muscular dystrophy patients are deletions of one or more exons in the DMD gene. The occurrence of deletions is slightly higher in Becker muscular dystrophy patients. Duplications are found in approximately 10% of Duchenne muscular dystrophy patients and 20% of Becker muscular dystrophy patients.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.7% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).