Open Access Open Badges Research article

A novel custom high density-comparative genomic hybridization array detects common rearrangements as well as deep intronic mutations in dystrophinopathies

Matteo Bovolenta12, Marcella Neri12, Sergio Fini12, Marina Fabris12, Cecilia Trabanelli12, Anna Venturoli12, Elena Martoni12, Elena Bassi12, Pietro Spitali12, Simona Brioschi12, Maria S Falzarano12, Paola Rimessi12, Roberto Ciccone3, Emma Ashton4, Joanne McCauley4, Shu Yau4, Stephen Abbs4, Francesco Muntoni5, Luciano Merlini12, Francesca Gualandi12* and Alessandra Ferlini12

Author Affiliations

1 Sezione di Genetica Medica, University of Ferrara, Italy

2 U.O. Genetica Medica St. Anna Hospital, Italy

3 Sezione di Biologia generale e Genetica Medica, University of Pavia, Italy

4 DNA Laboratory, Genetics Centre, Guy's & St. Thomas NHS Foundation Trust, London, UK

5 UCL Institute of Child Health, Dubowitz Neuromuscular Centre, London, UK

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BMC Genomics 2008, 9:572  doi:10.1186/1471-2164-9-572

Published: 28 November 2008



The commonest pathogenic DMD changes are intragenic deletions/duplications which make up to 78% of all cases and point mutations (roughly 20%) detectable through direct sequencing. The remaining mutations (about 2%) are thought to be pure intronic rearrangements/mutations or 5'-3' UTR changes. In order to screen the huge DMD gene for all types of copy number variation mutations we designed a novel custom high density comparative genomic hybridisation array which contains the full genomic region of the DMD gene and spans from 100 kb upstream to 100 kb downstream of the 2.2 Mb DMD gene.


We studied 12 DMD/BMD patients who either had no detectable mutations or carried previously identified quantitative pathogenic changes in the DMD gene. We validated the array on patients with previously known mutations as well as unaffected controls, we identified three novel pure intronic rearrangements and we defined all the mutation breakpoints both in the introns and in the 3' UTR region. We also detected a novel polymorphic intron 2 deletion/duplication variation. Despite the high resolution of this approach, RNA studies were required to confirm the functional significance of the intronic mutations identified by CGH. In addition, RNA analysis identified three intronic pathogenic variations affecting splicing which had not been detected by the CGH analysis.


This novel technology represents an effective high throughput tool to identify both common and rarer DMD rearrangements. RNA studies are required in order to validate the significance of the CGH array findings. The combination of these tools will fully cover the identification of causative DMD rearrangements in both coding and non-coding regions, particularly in patients in whom standard although extensive techniques are unable to detect a mutation.