Molecular combing reveals allelic combinations in facioscapulohumeral dystrophy

Nguyen, Karine; Walrafen, Pierre; Bernard, R.; Attarian, Shahram; Chaix, C; Vovan, Catherine; Renard, Emilie; Dufrane, Nathalie; Pouget, Jean; Vannier, Anne; Bensimon, Aaron; Lévy, Nicolas

doi:10.1002/ana.22513

Cited by 46 publications

(54 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Individual genetic polymorphisms could occur not only in the 4q35 region where they might affect DUX4 expression but also in any of the many genes shown to be deregulated in FSHD muscles. SNPs have been well studied in 4q35 but large polymorphisms have only started to be investigated by a combination of fluorescent in situ hybridization and DNA combing demonstrating unexpected rearrangements in this subtelomeric region (Nguyen et al 2011). Another source of heterogeneity is the biopsy: i.e.…”

Section: Resultsmentioning

confidence: 99%

Facioscapulohumeral muscular dystrophy (FSHD): an enigma unravelled?

et al. 2011

View full text Add to dashboard Cite

Facioscapulohumeral muscular dystrophy (FS HD) is the third most common muscular dystrophy after the dystrophinopathies and myotonic dystrophy and is associated with a typical pattern of muscle weakness. Most patients with FSHD carry a large deletion in the polymorphic D4Z4 macrosatellite repeat array at 4q35 and present with 1-10 repeats whereas non-affected individuals possess 11-150 repeats. An almost identical repeat array is present at 10q26 and the high sequence identity between these two arrays can cause difficulties in molecular diagnosis. Each 3.3-kb D4Z4 unit contains a DUX4 (double homeobox 4) gene that, among others, is activated upon contraction of the 4q35 repeat array due to the induction of chromatin remodelling of the 4qter region. A number of 4q subtelomeric sequence variants are now recognised, although FSHD only occurs in association with three 'permissive' haplotypes, each of which is associated with a polyadenylation signal located immediately distal of the last D4Z4 unit. The resulting poly-A tail appears to stabilise DUX4 mRNAs transcribed from this most distal D4Z4 unit in FSHD muscle cells. Synthesis of both the DUX4 transcripts and protein in FSHD muscle cells induces significant cell toxicity. DUX4 is a transcription factor that may target several genes which results in a deregulation cascade which inhibits myogenesis, sensitises cells to oxidative stress and induces muscle atrophy, thus recapitulating many of the key molecular features of FSHD.

show abstract

Section: Resultsmentioning

confidence: 99%

Facioscapulohumeral muscular dystrophy (FSHD): an enigma unravelled?

et al. 2011

View full text Add to dashboard Cite

show abstract

“…After combing, the DNA was bound to the coverslip by incubating overnight at 68°C. Fluorescence hybridization was performed on combed DNA using a set of six probes targeting the D4Z4 repeat array and its flanking regions to measure the number of D4Z4 repeats and to identify the specific chr 4 and chr 10 and haplotypes as described previously [34]. The probes were synthesized from plasmids containing the probe sequence by random priming and labeled using biotin, digoxigenin, or Alex Fluor 488 haptens.…”

Section: Dna Molecular Combing Of the 4q35 And 10q26 Allelesmentioning

confidence: 99%

“…The FSHDCombing Test™ was performed as described previously [34] with the following modifications. Agarose plugs were melted and digested with β-agarase overnight.…”

Section: Dna Molecular Combing Of the 4q35 And 10q26 Allelesmentioning

confidence: 99%

“…cells with two different genotypes) or rearrangements [33]. DNA molecular combing (MC) hybridizes multi-color DNA probes onto uniformly stretched DNA fiber and accurately identifies the 4qA and other alleles [34]. The precise measurement of the D4Z4 repeat motif by DNA combing may help correlate the size of the contracted 4qA allele with clinical features.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular combing compared to Southern blot for measuring D4Z4 contractions in FSHD

Vasale

Boyar

Jocson

et al. 2015

Neuromuscular Disorders

Self Cite

View full text Add to dashboard Cite

“…Examples of such genomic areas are the D4Z4 repeat array, which is related to Facioscapulohumeral muscular dystrophy (FSHD) (22), and the breast cancer-related genes BRCA1 and BRCA2 (23); these genes extend between 80 and 250 kbp and are known to have various pathogenic point mutations and structural rearrangements (24,25). To facilitate early diagnosis of malignant transformation, genomic mutations must be detected when only a small population of cells is transformed.…”

Section: Discussionmentioning

confidence: 99%

Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping

Gabrieli

Sharim

Michaeli

et al. 2017

Preprint

View full text Add to dashboard Cite

Variations in the genetic code, from single point mutations to large structural or copy number alterations, influence susceptibility, onset, and progression of genetic diseases and tumor transformation. Next-generation sequencing analysis is unable to reliably capture aberrations larger than the typical sequencing read length of several hundred bases. Long-read, singlemolecule sequencing methods such as SMRT and nanopore sequencing can address larger variations, but require costly whole genome analysis. Here we describe a method for isolation and enrichment of a large genomic region of interest for targeted analysis based on Cas9 excision of two sites flanking the target region and isolation of the excised DNA segment by pulsed field gel electrophoresis. The isolated target remains intact and is ideally suited for optical genome mapping and long-read sequencing at high coverage. In addition, analysis is performed directly on native genomic DNA that retains genetic and epigenetic composition without amplification bias. This method enables detection of mutations and structural variants as well as detailed analysis by generation of hybrid scaffolds composed of optical maps and sequencing data at a fraction of the cost of whole genome sequencing.

show abstract

Molecular combing reveals allelic combinations in facioscapulohumeral dystrophy

Abstract: MC enables the detailed exploration of the FSHD locus and accurate diagnosis of FSHD, the first Mendelian disease to benefit from this technique. MC is also likely to be applicable to other copy number-variant or repeat expansion-associated human diseases.

Cited by 46 publications

References 24 publications

Facioscapulohumeral muscular dystrophy (FSHD): an enigma unravelled?

Facioscapulohumeral muscular dystrophy (FSHD): an enigma unravelled?

Molecular combing compared to Southern blot for measuring D4Z4 contractions in FSHD

Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping

Contact Info

Product

Resources

About