Detecting copy number variations in autosomal recessive limb-girdle muscular dystrophies using a multiplex ligation-dependent probe amplification (MLPA) assay

Pathogenic mutations in the four sarcoglycan genes, designated SGCA, SGCB, SGCD and SGCG, are responsible for a subgroup of autosomal, recessive limb-girdle muscular dystrophies (LGMD 2C–F), also called sarcoglycanopathies. For the present study, we designed a multiplex ligation-dependent probe amplification (MLPA) assay, targeting all 30 coding exons and a non-coding exon of these four genes. The assay uses synthetic probes and two colours, such that as many as 28 probes can be combined into one reaction. The set of probes was established for routine application, in order to diagnostically screen patients for large duplications or deletions. In 14 of the 94 cases (15%) tested, we detected changes in copy number. Mutations in gene SGCG accounted for 7 of the 94 cases (8%), suggesting that the size of the gene makes it vulnerable to large exonic deletions. The results suggested that all cases of sarcoglycanopathy should be screened for changes in copy number. The MLPA was shown to be a rapid, robust and reliable method to screen for copy number variations (CNVs). The present synthetic probe-approach overcomes the limitations associated with cloning procedures and is particularly applicable to a range of diseases for which the number of patients to be tested is small.