Identification of a deep intronic mutation in the COL6A2 gene by a novel custom oligonucleotide CGH array designed to explore allelic and genetic heterogeneity in collagen VI-related myopathies

• Main Authors: Merlini Luciano, Bertini Enrico, Mercuri Eugenio, Grumati Paolo, Fabris Marina, Sabatelli Patrizia, Urciuolo Anna, Martoni Elena, Neri Marcella, Bovolenta Matteo, Bonaldo Paolo, Ferlini Alessandra, Gualandi Francesca
• Format: Article
• Language: English
• Published: BMC 2010-03-01
• Series: BMC Medical Genetics
• Online Access: http://www.biomedcentral.com/1471-2350/11/44

<p>Abstract</p> <p>Background</p> <p>Molecular characterization of collagen-VI related myopathies currently relies on standard sequencing, which yields a detection rate approximating 75-79% in Ullrich congenital muscular dystrophy (UCMD) and 60-65% in Bethlem myopathy (BM) patients as PCR-based techniques tend to miss gross genomic rearrangements as well as copy number variations (CNVs) in both the coding sequence and intronic regions.</p> <p>Methods</p> <p>We have designed a custom oligonucleotide CGH array in order to investigate the presence of CNVs in the coding and non-coding regions of <it>COL6A1, A2, A3, A5 </it>and <it>A6 </it>genes and a group of genes functionally related to collagen VI. A cohort of 12 patients with UCMD/BM negative at sequencing analysis and 2 subjects carrying a single <it>COL6 </it>mutation whose clinical phenotype was not explicable by inheritance were selected and the occurrence of allelic and genetic heterogeneity explored.</p> <p>Results</p> <p>A deletion within intron 1A of the <it>COL6A2 </it>gene, occurring in compound heterozygosity with a small deletion in exon 28, previously detected by routine sequencing, was identified in a BM patient. RNA studies showed monoallelic transcription of the <it>COL6A2 </it>gene, thus elucidating the functional effect of the intronic deletion. No pathogenic mutations were identified in the remaining analyzed patients, either within COL6A genes, or in genes functionally related to collagen VI.</p> <p>Conclusions</p> <p>Our custom CGH array may represent a useful complementary diagnostic tool, especially in recessive forms of the disease, when only one mutant allele is detected by standard sequencing. The intronic deletion we identified represents the first example of a pure intronic mutation in <it>COL6A </it>genes.</p>