Analysis of complex structural variants in the DMD gene in one family

Luce, Leonela Natalia; Abelleyro, Miguel Martín; Carcione, Micaela; Mazzanti, Chiara Maria; Rossetti, Liliana Carmen; Radic, Pamela; Szijan, Irene; Menazzi, Sebastián; Francipane, Liliana; Nevado, Julián; Lapunzina, Pablo; Brasi, Carlos Daniel de; Giliberto, Florencia

doi:10.1016/j.nmd.2020.11.015

Cited by 5 publications

(4 citation statements)

References 43 publications

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“…In DMD/BMD patients, complex structure variations were not rare to be detected by MLPA method, including the concurrence of exons deletion and duplication, and the noncontiguous deletion or duplication of DMD exons (21,22). However, the double mutations on one allele were rare (23), but the real recombination of the DMD gene was tough to be revealed by MLPA or short-read sequencing methods, thus very few of the previous studies illustrated the underlying sequence of the complex structure variation in DMD (24).…”

Section: Discussionmentioning

confidence: 99%

Captured long-read sequecing provides an efficient and accurate method for molecular diagnosis of Duchenne and Becker muscular dystrophies

Ling

Dai

Chang

et al. 2022

Preprint

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Background: Duchenne and Becker muscular dystrophies are not caused by deletions and duplications in the dystrophin (DMD) gene alone. A number of small and complex mutations in DMD were being found by multiple methods combined screening, including the next generation sequencing. However, there is still absent an effective method that could detect all types the potential variants in DMD. Therefore, in this study we explored a one-step detection method for DMD gene mutation based on long-read sequencing technology. Methods: A whole DMD gene panel including 20kb flanking sequences of the up and down stream of the DMD gene was designed. Pacific Biosciences and Oxford Nanopore Technologies were used to evaluate the capture and sequencing performance of the panel. A total of 129 subjects were selected for single-blind deep investigation and validation. Results: The results demonstrated that the long-read sequencing based DMD gene panel could integrally and accurately detect the multiple types of the variants in one-step. The noncontiguous variants were definitively corrected and attributed to translocation or inversion. Meanwhile, the micro insertion and deletion and the single nucleotide variants, especially the deep intronic variants, could be detected exactly compared with short-read sequencing technologies. Additionally, the captured long-read sequencing method could attain higher accuracy in female carrier mutation detection. Conclusion: This study illustrated that captured long-read sequencing could uncover the real features of DMD rearrangements via the effective junction reads analysis, and provide a complete and precise insight into the DMD gene mutation. Further, improve the molecular treatment of DMD/BMDin a base-pair resolution.

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Section: Discussionmentioning

confidence: 99%

Captured long-read sequecing provides an efficient and accurate method for molecular diagnosis of Duchenne and Becker muscular dystrophies

Ling

Dai

Chang

et al. 2022

Preprint

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“…Baskin et al [ 18 ] used a combination of MLPA, mRNA transcript analysis, array comparative hybridization arrays, and breakpoint sequence analysis to analyze the structure rearrangements and breakpoints of the DMD gene. Luce et al [ 19 ] used a multi-technique algorithm, including MLPA, microarrays, and next-generation whole-genome sequencing for the molecular characterization of complex structural variants in the DMD gene. Recently, long-read sequencing and Sanger sequencing revealed that the duplication of exons 56–61 in the DMD gene was a tandem repeat in a patient with DMD and that duplication occurred outside the DMD gene in an asymptomatic male [ 16 ].…”

Section: Discussionmentioning

confidence: 99%

Reclassification of DMD Duplications as Benign: Recommendations for Cautious Interpretation of Variants Identified in Prenatal Screening

Meng

et al. 2022

Genes

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Duplications are the main type of dystrophin gene (DMD) variants, which typically cause dystrophinopathies such as Duchenne muscular dystrophy and Becker muscular dystrophy. Maternally inherited exon duplication in DMD in fetuses is a relatively common finding of genetic screening in clinical practice. However, there is no standard strategy for interpretation of the pathogenicity of DMD duplications during prenatal screening, especially for male fetuses, in which maternally inherited pathogenic DMD variants more frequently cause dystrophinopathies. Here, we report three non-contiguous DMD duplications identified in a woman and her male fetus during prenatal screening. Multiplex ligation probe amplification and long-read sequencing were performed on the woman and her family members to verify the presence of DMD duplications. Structural rearrangements in the DMD gene were mapped by long-read sequencing, and the breakpoint junction sequences were validated using Sanger sequencing. The woman and her father carried three non-contiguous DMD duplications. Long-read and Sanger sequencing revealed that the woman’s father carried an intact DMD copy and a complex structural rearrangement of the DMD gene. Therefore, we reclassified these three non-contiguous DMD duplications, one of which is listed as pathogenic, as benign. We postulate that breakpoint analysis should be performed on identified DMD duplication variants, and the pathogenicity of the duplications found during prenatal screening should be interpreted cautiously for clinical prediction and genetic/reproductive counseling.

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“…All relevant F9 sequences were analysed by PCR amplification, according to Radic et al 16 . SNP‐array analysis was performed, using the CytoSNP850K platform (Illumina, San Diego, CA) according to Luce et al 17 …”

Section: Methodsmentioning

confidence: 99%

“…All relevant F9 sequences were analysed by PCR amplification, according to Radic et al 16 SNP-array analysis was performed, using the CytoSNP850K platform (Illumina, San Diego, CA) according to Luce et al 17 Case-specific sequence-tagged sites (STS) were designed to refine a delimitation of each deletion breakpoint. Sets of 3 or 4 primer pairs were used from each positive-negative SNP interval in the SNP array (Supplementary Figure SF2; Supplementary Table ST1).…”

Section: Molecular Genotypingmentioning

confidence: 99%

Haemophilia B, severe childhood obesity and other extra‐haematological features associated with similar 4Mb‐deletions on Xq27: Clinical findings, molecular insights and literature update

et al. 2023

Self Cite

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Introduction: Haemophilia B (HB) is associated with pathogenic variants in F9. Hemizygous deletions encompassing the entire F9 and proximate genes may express extra-haematological clinical phenotypes. Aim: To analyse the genotype/phenotype correlations in two unrelated boys with severe early childhood obesity (SCO), global developmental delay (GDD) and similar bleeding phenotype associated with comparable Xq27 deletions spanning the entire F9 and proximate genes, and characterise the pathogenic events estimating the most likely mutational mechanism involved. Methods: Entire F9-deletions were detected in three hemizygous unrelated probands with HB: two cases, C#1/C#2, presented SCO and GDD and a control patient (Co), who only had severe bleeding symptoms. Dense SNP-array and case-specific STS walking scan allowed characterisation of the deletion breakpoints. Extensive use of bioinformatics, statistics and clinical databases allowed the investigation of genotype-phenotype associations. Results: Patients C#1/C#2 and Co resulted in a complete F9 and additional gene deletions of variable extensions on Xq26.3-Xq27.2 (C#1/C#2/Co: 4.3Mb/3.9Mb/160Kb). C#1/C#2 common deleted gene SOX3 is directly associated with SCO, GDD and pituitary hypothyroidism (PH) whilst C#2 extra-deleted gene MAGEC2 indirectly relates to anal atresia (AA). Breakpoint analysis revealed the involvement of the mechanisms of Alu/Alu recombination for the first time in HB and non-homologous or alternative end-joining. Conclusion: Our results represent the first report of unrelated patients with HB, SCO and GDD. This study and the literature update expand the spectrum of clinical findings

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Analysis of complex structural variants in the DMD gene in one family

Cited by 5 publications

References 43 publications

Captured long-read sequecing provides an efficient and accurate method for molecular diagnosis of Duchenne and Becker muscular dystrophies

Captured long-read sequecing provides an efficient and accurate method for molecular diagnosis of Duchenne and Becker muscular dystrophies

Reclassification of DMD Duplications as Benign: Recommendations for Cautious Interpretation of Variants Identified in Prenatal Screening

Haemophilia B, severe childhood obesity and other extra‐haematological features associated with similar 4Mb‐deletions on Xq27: Clinical findings, molecular insights and literature update

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