Microarray-based mutation detection in the<i>dystrophin</i>gene

Hegde, Madhuri; Chin, Ephrem; Mullé, Jennifer G.; Okou, David T.; Warren, Stephen T.; Zwick, Michael E.

doi:10.1002/humu.20831

Cited by 108 publications

(97 citation statements)

References 35 publications

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“…In conclusion, this large survey of 50 patients confirmed the previous observations [10][11][12][13] that array-CGH is a reliable and effective tool in detecting simple and complex DMD rearrangements. This approach offers some advantages over exon-based detection methods as it can identify pure intronic pathogenic events and it allows precise delineation of rearrangements, some of which may affect the splicing process.…”

Section: Discussionsupporting

confidence: 87%

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

et al. 2012

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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.

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Section: Discussionsupporting

confidence: 87%

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

et al. 2012

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“…10,11,36,37 It was believed that a causative mutation in the dystrophin gene could not be identified in approximately 1 to 2% of DMD/BMD patients. 12 In contrast to previous studies, our perfect mutation detection rate became possible by conducting dystrophin cDNA or chromosomal analysis. Without these analyses, our mutation detection rate decreased by nearly 2%, that is, down to the previously accepted detection rate.…”

Section: Discussionmentioning

confidence: 96%

“…Without these analyses, our mutation detection rate decreased by nearly 2%, that is, down to the previously accepted detection rate. 12 We propose that similarly extensive mutation analysis should be performed to identify the responsible mutation when dystrophin deficiency has been confirmed.…”

Section: Discussionmentioning

confidence: 99%

“…10 In spite of technological advances in mutation analysis, a complete mutation spectrum has not been established in a large cohort, leaving some percentage of cases undiagnosed, 11 and the dystrophin gene remain uncharacterized in some percentage of cases. 12 Identifying a dystrophin mutation in all cases would permit a clinical diagnosis as the basis for proper genetic counseling, and is also a precondition for future molecular therapies, such as correction of the reading frame shift by induction of exon skipping, or suppression of nonsense mutation during translation. [13][14][15] In Japan, however, there is no large-scale database for mutations of dystrophinopathy.…”

Section: Duchenne Muscular Dystrophy (Dmd; Mim (Online Mendelianmentioning

confidence: 99%

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Mutation spectrum of the dystrophin gene in 442 Duchenne/Becker muscular dystrophy cases from one Japanese referral center

et al. 2010

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Recent developments in molecular therapies for Duchenne muscular dystrophy (DMD) demand accurate genetic diagnosis, because therapies are mutation specific. The KUCG (Kobe University Clinical Genetics) database for DMD and Becker muscular dystrophy is a hospital-based database comprising 442 cases. Using a combination of complementary DNA (cDNA) and chromosome analysis in addition to conventional genomic DNA-based method, mutation detection was successfully accomplished in all cases, and the largest mutation database of Japanese dystrophinopathy was established. Among 442 cases, deletions and duplications encompassing one or more exons were identified in 270 (61%) and 38 (9%) cases, respectively. Nucleotide changes leading to nonsense mutations or disrupting a splice site were identified in 69 (16%) or 24 (5%) cases, respectively. Small deletion/insertion mutations were identified in 34 (8%) cases. Remarkably, two retrotransposon insertion events were also identified. Dystrophin cDNA analysis successfully revealed novel transcripts with a pseudoexon created by a single-nucleotide change deep within an intron in four cases. X-chromosome abnormalities were identified in two cases. The reading frame rule was upheld for 93% of deletion and 66% of duplication mutation cases. For the application of molecular therapies, induction of exon skipping was deemed the first priority for dystrophinopathy treatment. At one Japanese referral center, the hospital-based mutation database of the dystrophin gene was for the first time established with the highest levels of quality and patient's number.

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“…3 Most laboratories perform two or more steps to detect mutations in a suspected DMD patient. Multiplex ligationdependent probe amplification (MLPA) or array comparative genome hybridization (aCGH) is used to detect large deletions/duplications; 4,5 if no deletion/duplication is detected, Sanger sequencing of all the DMD exons is performed. 6,7 However, in addition to the high cost and time requirements of the entire process, the results can be inconclusive.…”

Section: Introductionmentioning

confidence: 99%

Targeted next-generation sequencing as a comprehensive test for patients with and female carriers of DMD/BMD: a multi-population diagnostic study

Wei

Dai

et al. 2013

Eur J Hum Genet

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Duchenne and Becker muscular dystrophies (DMD/BMD) are the most commonly inherited neuromuscular disease. However, accurate and convenient molecular diagnosis cannot be achieved easily because of the enormous size of the dystrophin gene and complex causative mutation spectrum. Such traditional methods as multiplex ligation-dependent probe amplification plus Sanger sequencing require multiple steps to fulfill the diagnosis of DMD/BMD. Here, we introduce a new single-step method for the genetic analysis of DMD patients and female carriers in real clinical settings and demonstrate the validation of its accuracy. A total of 89 patients, 18 female carriers and 245 non-DMD patients were evaluated using our targeted NGS approaches. Compared with traditional methods, our new method yielded 99.99% specificity and 98.96% sensitivity for copy number variations detection and 100% accuracy for the identification of single-nucleotide variation mutations. Additionally, this method is able to detect partial deletions/duplications, thus offering precise personal DMD gene information for gene therapy. We detected novel partial deletions of exons in nine samples for which the breakpoints were located within exonic regions. The results proved that our new method is suitable for routine clinical practice, with shorter turnaround time, higher accuracy, and better insight into comprehensive genetic information (detailed breakpoints) for ensuing gene therapy.

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Microarray-based mutation detection in thedystrophingene

Cited by 108 publications

References 35 publications

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

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

Mutation spectrum of the dystrophin gene in 442 Duchenne/Becker muscular dystrophy cases from one Japanese referral center

Targeted next-generation sequencing as a comprehensive test for patients with and female carriers of DMD/BMD: a multi-population diagnostic study

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