Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>)
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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MDPI AG
2021-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/1/59 |
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| author | Ana Gonçalves Ana Fortuna Yavuz Ariyurek Márcia E. Oliveira Goreti Nadais Jorge Pinheiro Johan T. den Dunnen Mário Sousa Jorge Oliveira Rosário Santos |
| author_facet | Ana Gonçalves Ana Fortuna Yavuz Ariyurek Márcia E. Oliveira Goreti Nadais Jorge Pinheiro Johan T. den Dunnen Mário Sousa Jorge Oliveira Rosário Santos |
| author_sort | Ana Gonçalves |
| collection | DOAJ |
| 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 <i>DMD</i> gene. Muscle <i>DMD</i> 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 <i>DMD</i> intron 74 and a region located upstream of the <i>PRDX4</i> gene. Breakpoint PCR and Sanger sequencing confirmed the presence of a ~8 Mb genomic inversion. Aberrant <i>DMD</i> transcripts were subsequently identified, some of which contained segments from the region upstream of <i>PRDX4</i>. 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. |
| first_indexed | 2024-03-10T03:40:34Z |
| format | Article |
| id | doaj.art-835cd4b7e6a64425bb677ae1104fc224 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T03:40:34Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-835cd4b7e6a64425bb677ae1104fc2242023-11-23T11:33:59ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-12-012315910.3390/ijms23010059Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>)Ana Gonçalves0Ana Fortuna1Yavuz Ariyurek2Márcia E. Oliveira3Goreti Nadais4Jorge Pinheiro5Johan T. den Dunnen6Mário Sousa7Jorge Oliveira8Rosário Santos9Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto Magalhães, Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, PortugalUnidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS) e Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Universidade do Porto, 4050-313 Porto, PortugalLeiden Genome Technology Center, Leiden University Medical Center, 2333 ZA Leiden, The NetherlandsUnidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto Magalhães, Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, PortugalServiço de Neurologia, Centro Hospitalar de São João, 4200-319 Porto, PortugalServiço de Anatomia Patológica, Centro Hospitalar de São João, 4200-319 Porto, PortugalLeiden Genome Technology Center, Leiden University Medical Center, 2333 ZA Leiden, The NetherlandsUnidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS) e Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Universidade do Porto, 4050-313 Porto, PortugalUnidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto Magalhães, Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, PortugalUnidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto Magalhães, Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, PortugalWhile 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 <i>DMD</i> gene. Muscle <i>DMD</i> 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 <i>DMD</i> intron 74 and a region located upstream of the <i>PRDX4</i> gene. Breakpoint PCR and Sanger sequencing confirmed the presence of a ~8 Mb genomic inversion. Aberrant <i>DMD</i> transcripts were subsequently identified, some of which contained segments from the region upstream of <i>PRDX4</i>. 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.https://www.mdpi.com/1422-0067/23/1/59DMDwhole genome sequencing (WGS)inversiondystrophinopathies |
| spellingShingle | Ana Gonçalves Ana Fortuna Yavuz Ariyurek Márcia E. Oliveira Goreti Nadais Jorge Pinheiro Johan T. den Dunnen Mário Sousa Jorge Oliveira Rosário Santos Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>) International Journal of Molecular Sciences DMD whole genome sequencing (WGS) inversion dystrophinopathies |
| title | Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>) |
| title_full | Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>) |
| title_fullStr | Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>) |
| title_full_unstemmed | Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>) |
| title_short | Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>) |
| title_sort | integrating whole genome sequencing in clinical genetics a novel disruptive structural rearrangement identified in the dystrophin gene i dmd i |
| topic | DMD whole genome sequencing (WGS) inversion dystrophinopathies |
| url | https://www.mdpi.com/1422-0067/23/1/59 |
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