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Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (DMD)

While in most patients the identification of genetic alterations causing dystrophinopathies is a relatively straightforward task, a significant number require genomic and transcriptomic approaches that go beyond a routine diagnostic set-up. In this work, we present a Becker Muscular Dystrophy patien...

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Autores principales: Gonçalves, Ana, Fortuna, Ana, Ariyurek, Yavuz, Oliveira, Márcia E., Nadais, Goreti, Pinheiro, Jorge, den Dunnen, Johan T., Sousa, Mário, Oliveira, Jorge, Santos, Rosário
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8744749/
https://www.ncbi.nlm.nih.gov/pubmed/35008485
http://dx.doi.org/10.3390/ijms23010059
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author Gonçalves, Ana
Fortuna, Ana
Ariyurek, Yavuz
Oliveira, Márcia E.
Nadais, Goreti
Pinheiro, Jorge
den Dunnen, Johan T.
Sousa, Mário
Oliveira, Jorge
Santos, Rosário
author_facet Gonçalves, Ana
Fortuna, Ana
Ariyurek, Yavuz
Oliveira, Márcia E.
Nadais, Goreti
Pinheiro, Jorge
den Dunnen, Johan T.
Sousa, Mário
Oliveira, Jorge
Santos, Rosário
author_sort Gonçalves, Ana
collection PubMed
description While in most patients the identification of genetic alterations causing dystrophinopathies is a relatively straightforward task, a significant number require genomic and transcriptomic approaches that go beyond a routine diagnostic set-up. In this work, we present a Becker Muscular Dystrophy patient with elevated creatinine kinase levels, progressive muscle weakness, mild intellectual disability and a muscle biopsy showing dystrophic features and irregular dystrophin labelling. Routine molecular techniques (Southern-blot analysis, multiplex PCR, MLPA and genomic DNA sequencing) failed to detect a defect in the DMD gene. Muscle DMD transcript analysis (RT-PCR and cDNA-MLPA) showed the absence of exons 75 to 79, seen to be present at the genomic level. These results prompted the application of low-coverage linked-read whole-genome sequencing (WGS), revealing a possible rearrangement involving DMD intron 74 and a region located upstream of the PRDX4 gene. Breakpoint PCR and Sanger sequencing confirmed the presence of a ~8 Mb genomic inversion. Aberrant DMD transcripts were subsequently identified, some of which contained segments from the region upstream of PRDX4. Besides expanding the mutational spectrum of the disorder, this study reinforces the importance of transcript analysis in the diagnosis of dystrophinopathies and shows how WGS has a legitimate role in clinical laboratory genetics.
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spelling pubmed-87447492022-01-11 Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (DMD) Gonçalves, Ana Fortuna, Ana Ariyurek, Yavuz Oliveira, Márcia E. Nadais, Goreti Pinheiro, Jorge den Dunnen, Johan T. Sousa, Mário Oliveira, Jorge Santos, Rosário Int J Mol Sci Case Report While in most patients the identification of genetic alterations causing dystrophinopathies is a relatively straightforward task, a significant number require genomic and transcriptomic approaches that go beyond a routine diagnostic set-up. In this work, we present a Becker Muscular Dystrophy patient with elevated creatinine kinase levels, progressive muscle weakness, mild intellectual disability and a muscle biopsy showing dystrophic features and irregular dystrophin labelling. Routine molecular techniques (Southern-blot analysis, multiplex PCR, MLPA and genomic DNA sequencing) failed to detect a defect in the DMD gene. Muscle DMD transcript analysis (RT-PCR and cDNA-MLPA) showed the absence of exons 75 to 79, seen to be present at the genomic level. These results prompted the application of low-coverage linked-read whole-genome sequencing (WGS), revealing a possible rearrangement involving DMD intron 74 and a region located upstream of the PRDX4 gene. Breakpoint PCR and Sanger sequencing confirmed the presence of a ~8 Mb genomic inversion. Aberrant DMD transcripts were subsequently identified, some of which contained segments from the region upstream of PRDX4. Besides expanding the mutational spectrum of the disorder, this study reinforces the importance of transcript analysis in the diagnosis of dystrophinopathies and shows how WGS has a legitimate role in clinical laboratory genetics. MDPI 2021-12-22 /pmc/articles/PMC8744749/ /pubmed/35008485 http://dx.doi.org/10.3390/ijms23010059 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Case Report
Gonçalves, Ana
Fortuna, Ana
Ariyurek, Yavuz
Oliveira, Márcia E.
Nadais, Goreti
Pinheiro, Jorge
den Dunnen, Johan T.
Sousa, Mário
Oliveira, Jorge
Santos, Rosário
Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (DMD)
title Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (DMD)
title_full Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (DMD)
title_fullStr Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (DMD)
title_full_unstemmed Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (DMD)
title_short Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (DMD)
title_sort integrating whole-genome sequencing in clinical genetics: a novel disruptive structural rearrangement identified in the dystrophin gene (dmd)
topic Case Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8744749/
https://www.ncbi.nlm.nih.gov/pubmed/35008485
http://dx.doi.org/10.3390/ijms23010059
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