Comprehensive oligonucleotide array-comparative genomic hybridization analysis: new insights into the molecular pathology of the DMD gene

Abstract

We report on the effectiveness of a custom-designed oligonucleotide-based comparative genomic hybridization microarray (array-CGH) to interrogate copy number across the entire 2.2-Mb genomic region of the DMD gene and its applicability in diagnosis. The high-resolution array-CGH, we developed, successfully detected a series of 42 previously characterized large rearrangements of various size, localization and type (simple or complex deletions, duplications, triplications) and known intronic CNVs/Indels. Moreover, the technique succeeded in identifying a small duplication of only 191 bp in one patient previously negative for DMD mutation. Accurate intronic breakpoints localization by the technique enabled subsequent junction fragments identification by sequencing in 86% of cases (all deletion cases and 62.5% of duplication cases). Sequence examination of the junctions supports a role of microhomology-mediated processes in the occurrence of DMD large rearrangements. In addition, the precise knowledge of the sequence context at the breakpoints and analysis of the resulting consequences on maturation of pre-mRNA contribute to elucidating the cause of discrepancies in phenotype/genotype correlations in some patients. Thereby, the array-CGH proved to be a highly efficient and reliable diagnostic tool, and the new data it provides will have many potential implications in both, clinics and research.

Exonic rearrangements in DMD in Chinese Han individuals affected with Duchenne and Becker muscular dystrophies

“…There are at least five categories of mutational mechanisms known to initiate genomic recombination: (a) homologous recombination including nonallelic homologous recombination, gene conversion, single‐strand annealing, and break‐induced replication, (b) nonhomologous end joining (NHEJ), (c) microhomology‐mediated replication‐dependent recombination (MMRDR), (d) long interspersed element‐1‐mediated retrotransposition, and (e) telomere healing (Chen, Cooper, Ferec, Kehrer‐Sawatzki, & Patrinos, ). Among these, MMRDR and NHEJ are the two main mechanisms involved in DMD intragenic deletions (Ishmukhametova et al, ; Lieber, ; Oshima et al, ). MMRDR was hypothesized to cause replication fork stalling and template switching, which could induce complex deletion and duplication rearrangement (Lee, Carvalho, & Lupski, ).…”

Identification of a novel DMD duplication identified by a combination of MLPA and targeted exome sequencing

“…Duchenne muscular dystrophy (DMD), an X-linked recessive muscle-wasting disease, is caused by a mutation in the DMD gene that encodes the dystrophin protein [1, 2]. As the most common muscle disease in children, the incidence of DMD is 1 in 3500 live male births [3].…”

Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes

“…It is the first technology that allows determination of CNM boundaries precisely enough to guide targeted sequencing of breakpoints. 35 Possibility of high scale sequencing of breakpoints will bring real progress in understanding molecular mechanisms of rearrangements, searching for genotype–phenotype correlations and to guide certain therapeutic strategies.…”