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

Matteo Bovolenta, Marcella Neri, Elena Martoni, Anna Urciuolo, Patrizia Sabatelli, Marina Fabris, Paolo Grumati, Eugenio Mercuri, Enrico Bertini, Luciano Merlini, Paolo Bonaldo, Alessandra Ferlini, Francesca Gualandi

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number44
JournalBMC Medical Genetics
Volume11
Issue number1
DOIs
Publication statusPublished - Mar 19 2010

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Genetic Heterogeneity
Muscular Diseases
Oligonucleotide Array Sequence Analysis
Collagen
Mutation
Genes
varespladib methyl
Introns
Exons
Alleles
RNA
Phenotype
Polymerase Chain Reaction
Bethlem myopathy

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

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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. / 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.

In: BMC Medical Genetics, Vol. 11, No. 1, 44, 19.03.2010.

Research output: Contribution to journalArticle

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. / 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. In: BMC Medical Genetics. 2010 ; Vol. 11, No. 1.
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AU - Neri, Marcella

AU - Martoni, Elena

AU - Urciuolo, Anna

AU - Sabatelli, Patrizia

AU - Fabris, Marina

AU - Grumati, Paolo

AU - Mercuri, Eugenio

AU - Bertini, Enrico

AU - Merlini, Luciano

AU - Bonaldo, Paolo

AU - Ferlini, Alessandra

AU - Gualandi, Francesca

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N2 - 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.

AB - 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.

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