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Scarano C, Veneruso I, De Simone RR, Di Bonito G, Secondino A, D’Argenio V. The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences. Biomolecules 2024; 14:568. [PMID: 38785975 PMCID: PMC11117673 DOI: 10.3390/biom14050568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The understanding of the human genome has been greatly improved by the advent of next-generation sequencing technologies (NGS). Despite the undeniable advantages responsible for their widespread diffusion, these methods have some constraints, mainly related to short read length and the need for PCR amplification. As a consequence, long-read sequencers, called third-generation sequencing (TGS), have been developed, promising to overcome NGS. Starting from the first prototype, TGS has progressively ameliorated its chemistries by improving both read length and base-calling accuracy, as well as simultaneously reducing the costs/base. Based on these premises, TGS is showing its potential in many fields, including the analysis of difficult-to-sequence genomic regions, structural variations detection, RNA expression profiling, DNA methylation study, and metagenomic analyses. Protocol standardization and the development of easy-to-use pipelines for data analysis will enhance TGS use, also opening the way for their routine applications in diagnostic contexts.
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Affiliation(s)
- Carmela Scarano
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Iolanda Veneruso
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Rosa Redenta De Simone
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gennaro Di Bonito
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Angela Secondino
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di Val Cannuta 247, 00166 Roma, Italy
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Pickart AM, Martin AS, Gross BN, Dellefave-Castillo LM, McCallen LM, Nagaraj CB, Rippert AL, Schultz CP, Ulm EA, Armstrong N. Genetic counseling for the dystrophinopathies-Practice resource of the National Society of Genetic Counselors. J Genet Couns 2024. [PMID: 38682751 DOI: 10.1002/jgc4.1892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 05/01/2024]
Abstract
The dystrophinopathies encompass the phenotypically variable forms of muscular dystrophy caused by pathogenic variants in the DMD gene. The dystrophinopathies include the most common inherited muscular dystrophy among 46,XY individuals, Duchenne muscular dystrophy, as well as Becker muscular dystrophy and other less common phenotypic variants. With increased access to and utilization of genetic testing in the diagnostic and carrier setting, genetic counselors and clinicians in diverse specialty areas may care for individuals with and carriers of dystrophinopathy. This practice resource was developed as a tool for genetic counselors and other health care professionals to support counseling regarding dystrophinopathies, including diagnosis, health risks and management, psychosocial needs, reproductive options, clinical trials, and treatment. Genetic testing efforts have enabled genotype/phenotype correlation in the dystrophinopathies, but have also revealed unexpected findings, further complicating genetic counseling for this group of conditions. Additionally, the therapeutic landscape for dystrophinopathies has dramatically changed with several FDA-approved therapeutics, an expansive research pathway, and numerous clinical trials. Genotype-phenotype correlations are especially complex and genetic counselors' unique skill sets are useful in exploring and explaining this to families. Given the recent advances in diagnostic testing and therapeutics related to dystrophinopathies, this practice resource is a timely update for genetic counselors and other healthcare professionals involved in the diagnosis and care of individuals with dystrophinopathies.
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Affiliation(s)
- Angela M Pickart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ann S Martin
- Parent Project Muscular Dystrophy, Washington, District of Columbia, USA
| | - Brianna N Gross
- Department of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lisa M Dellefave-Castillo
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Leslie M McCallen
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Chinmayee B Nagaraj
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Alyssa L Rippert
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Elizabeth A Ulm
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Niki Armstrong
- Parent Project Muscular Dystrophy, Washington, District of Columbia, USA
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Perrin A, Van Goethem C, Thèze C, Puechberty J, Guignard T, Lecardonnel B, Lacourt D, Métay C, Isapof A, Whalen S, Ferreiro A, Arne-Bes MC, Quijano-Roy S, Nectoux J, Leturcq F, Richard P, Larrieux M, Bergougnoux A, Pellestor F, Koenig M, Cossée M. Long-Reads Sequencing Strategy to Localize Variants in TTN Repeated Domains. J Mol Diagn 2022; 24:719-726. [PMID: 35580751 DOI: 10.1016/j.jmoldx.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/23/2022] [Accepted: 04/18/2022] [Indexed: 11/19/2022] Open
Abstract
Titin protein is responsible for muscle elasticity. The TTN gene, composed of 364 exons, is subjected to extensive alternative splicing and leads to different isoforms expressed in skeletal and cardiac muscle. Variants in TTN are responsible for myopathies with a wide phenotypic spectrum and autosomal dominant or recessive transmission. The I-band coding domain, highly subject to alternative splicing, contains a three-zone block of repeated sequences with 99% homology. Sequencing and localization of variants in these areas are complex when using short-reads sequencing, a second-generation sequencing technique. We have implemented a protocol based on the third-generation sequencing technology (long-reads sequencing). This new method allows us to localize variants in these repeated areas to improve the diagnosis of TTN-related myopathies and offer the analysis of relatives in postnatal or in prenatal screening.
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Affiliation(s)
- Aurélien Perrin
- Molecular Diagnostic Laboratory, Montpellier University Hospital, Montpellier, France; PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Charles Van Goethem
- Molecular Diagnostic Laboratory, Montpellier University Hospital, Montpellier, France
| | - Corinne Thèze
- Molecular Diagnostic Laboratory, Montpellier University Hospital, Montpellier, France
| | - Jacques Puechberty
- Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Thomas Guignard
- Laboratoire de Génétique Chromosomique, Plateforme ChromoStem, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Bérénice Lecardonnel
- Laboratoire de Génétique Chromosomique, Plateforme ChromoStem, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Delphine Lacourt
- Molecular Diagnostic Laboratory, Montpellier University Hospital, Montpellier, France
| | - Corinne Métay
- Assistance Publique-Hôpitaux de Paris (AP-HP), UF Molecular Cardiogenetics and Myogenetics, Sorbonne Université and Sorbonne Université UPMC Paris 06-Inserm UMRS974, Research Center in Myology, Pitié-Salpêtrière Hospital, Paris, France
| | - Arnaud Isapof
- Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France, Service de Neuropédiatrie, Hôpital Trousseau, Paris, France
| | - Sandra Whalen
- Genetics and Cytogenetics Department, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpétrière, AP-HP, Paris, France
| | - Ana Ferreiro
- AP-HP, Centre de Référence des Pathologies Neuromusculaires Nord-Est-Ile de France, Institut de Myologie, GHU Pitié-Salpêtrière, Paris, France; Basic and Translational Myology Laboratory, Université de Paris BFA, UMR 8251, CNRS, Paris, France
| | | | - Susana Quijano-Roy
- AP-HP, GH Université Paris-Saclay, Neuromuscular Center, Child Neurology and ICU Department, Raymond Poincare Hospital, Garches, France; Université de Versailles, U1179 INSERM-UVSQ, Montigny, France
| | - Juliette Nectoux
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université de Paris, Paris, France
| | - France Leturcq
- Department of Genetics and Molecular Biology, AP-HP, Cochin Hospital, Paris, France
| | - Pascale Richard
- Assistance Publique-Hôpitaux de Paris (AP-HP), UF Molecular Cardiogenetics and Myogenetics, Sorbonne Université and Sorbonne Université UPMC Paris 06-Inserm UMRS974, Research Center in Myology, Pitié-Salpêtrière Hospital, Paris, France
| | - Marion Larrieux
- Molecular Diagnostic Laboratory, Montpellier University Hospital, Montpellier, France
| | - Anne Bergougnoux
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Franck Pellestor
- Laboratoire de Génétique Chromosomique, Plateforme ChromoStem, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Michel Koenig
- Molecular Diagnostic Laboratory, Montpellier University Hospital, Montpellier, France; PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Mireille Cossée
- Molecular Diagnostic Laboratory, Montpellier University Hospital, Montpellier, France; PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France.
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Li Q, Chen Z, Xiong H, Li R, Yu C, Meng J, Shi P, Kong X. Novel Partial Exon 51 Deletion in the Duchenne Muscular Dystrophy Gene Identified via Whole Exome Sequencing and Long-Read Whole-Genome Sequencing. Front Genet 2021; 12:762987. [PMID: 34899847 PMCID: PMC8662377 DOI: 10.3389/fgene.2021.762987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023] Open
Abstract
Duchenne muscular dystrophy (DMD), one of the most common progressive and severely disabling neuromuscular diseases in children, can be largely attributed to the loss of function of the DMD gene on chromosome Xp21.2-p21.1. This paper describes the case of a 10-year-old boy diagnosed with DMD. Whole exome sequencing confirmed the hypothesized large partial exonic deletion of c.7310-11543_7359del (chrX:g.31792260_31803852del) spanning exon 51 and intron 50 in DMD. This large deletion was verified to be de novo by PCR, and the two breakpoints were further confirmed by Sanger sequencing and long-read whole-genome sequencing. Notably, this partial exonic deletion was the only complex variation in the deep intron regions or intron–exon junction regions in DMD. In addition, the case study demonstrates the clinical importance of using multiple molecular genetic testing methods for the diagnosis of rare diseases.
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Affiliation(s)
- Qianqian Li
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhanni Chen
- Genokon Institute of Medical Science and Laboratory, Xiamen, China
| | - Hui Xiong
- Genokon Institute of Medical Science and Laboratory, Xiamen, China
| | - Ranran Li
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Chenguang Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Cardio-X Center, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Meng
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Panlai Shi
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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