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

• Published in: BMC medical genetics Vol. 11; no. 1; p. 44
• Main Authors: Bovolenta, Matteo, Neri, Marcella, Martoni, Elena, Urciuolo, Anna, Sabatelli, Patrizia, Fabris, Marina, Grumati, Paolo, Mercuri, Eugenio, Bertini, Enrico, Merlini, Luciano, Bonaldo, Paolo, Ferlini, Alessandra, Gualandi, Francesca
• Format: Journal Article
• Language: English
• Published: London BioMed Central 19.03.2010; BioMed Central Ltd; BMC
• Subjects: Adolescent; Adult; Alleles; Biomedical and Life Sciences; Biomedicine; Child; Child, Preschool; Cohort Studies; Collagen Type VI - genetics; Comparative Genomic Hybridization; Cytogenetics; DNA microarrays; Female; Fibroblasts - metabolism; Fibroblasts - pathology; Gene Deletion; Gene Dosage; Gene Function; Gene mutations; Genetic aspects; Genetic Heterogeneity; Genotype; Health aspects; Heterozygote; Human Genetics; Humans; Immunohistochemistry; Introns; Male; Middle Aged; Muscle diseases; Muscular Diseases - diagnosis; Muscular Diseases - genetics; Muscular Dystrophies - diagnosis; Muscular Dystrophies - genetics; Mutation; Oligonucleotide Array Sequence Analysis; Phenotype; Research Article; Risk factors; Italy; Club Foot; Comparative Genomic Hybridization; COL6 Gene; Comparative Genomic Hybridization Array; COL6A2 Gene
• ISSN: 1471-2350; 1471-2350
• DOI: 10.1186/1471-2350-11-44

Background 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. Methods We have designed a custom oligonucleotide CGH array in order to investigate the presence of CNVs in the coding and non-coding regions of COL6A1, A2, A3, A5 and A6 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 COL6 mutation whose clinical phenotype was not explicable by inheritance were selected and the occurrence of allelic and genetic heterogeneity explored. Results A deletion within intron 1A of the COL6A2 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 COL6A2 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. Conclusions 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 COL6A genes.