The Genetic Approach: Next-Generation Sequencing-Based Diagnosis of Congenital and Infantile Myopathies/Muscle Dystrophies

Abstract

The practical basis for massive parallel sequencing is described to help clinicians in choosing the most adequate diagnostic approach for childhood myopathies. The key quality feature for massive parallel sequencing is the sequence depth (coverage) as a prerequisite for variant identification and quantification of sequence copy numbers. Our experience with a next-generation sequencing gene panel for the analysis of muscular dystrophies/myopathies with infantile or juvenile onset resulted in the identification of pathogenic or likely pathogenic mutations in approximately 41% (of 141 patients), thus leading to a definitive diagnosis. A subset of patients shows an accumulation of “excess” heterozygous variants that may act as modifiers of the phenotype. Massive parallel sequencing has become a reliable and cost-effective method, but it requires exact clinical, bioptic, and/or radiologic information to evaluate the clinical relevance of possibly pathologic variants.

Keywords

congenital myopathy/muscular dystrophy - infantile myopathies/muscular dystrophies - gene panel analysis - variant classification

• References

• 1 Schuelke M, Øien NC, Oldfors A. Review: myopathology in the times of modern genetics. Neuropathol Appl Neurobiol 2017; 43: 44-61
• 2 Muscle Disease: Pathology and Genetics. 2nd ed. In: Goebel HH, Sewry CA, Weller RO. Chichester, UK: John Wiley & Sons; 2013. chap 3
• 3 Patient Register. https://www.treat-nmd.de/register/index.de.html. Accessed May 2, 2017
• 4 Liang WC, Tian X, Yuo CY. , et al. Comprehensive target capture/next-generation sequencing as a second-tier diagnostic approach for congenital muscular dystrophy in Taiwan. PLoS One 2017; 12 (02) e0170517
• 5 Kuhn M, Gläser D, Joshi PR. , et al. Utility of a next-generation sequencing-based gene panel investigation in German patients with genetically unclassified limb-girdle muscular dystrophy. J Neurol 2016; 263 (04) 743-750
• 6 Lévesque S, Auray-Blais C, Gravel E. , et al. Diagnosis of late-onset Pompe disease and other muscle disorders by next-generation sequencing. Orphanet J Rare Dis 2016; 11 (08) 8
• 7 Gorokhova S, Biancalana V, Lévy N, Laporte J, Bartoli M, Krahn M. Clinical massively parallel sequencing for the diagnosis of myopathies. Rev Neurol (Paris) 2015; 171 (6–7): 558-571
• 8 Kitamura Y, Kondo E, Urano M, Aoki R, Saito K. Target resequencing of neuromuscular disease-related genes using next-generation sequencing for patients with undiagnosed early-onset neuromuscular disorders. J Hum Genet 2016; 61 (11) 931-942
• 9 Richards S, Aziz N, Bale S. , et al; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015; 17 (05) 405-424
• 10 Wolf B, Kuonen P, Dandekar T, Atlan D. DNAseq workflow in a diagnostic context and an example of a user-friendly implementation. Biomed Res Int 2015; 2015: 403497
• 11 Marelli C, Guissart C, Hubsch C. , et al. Mini-exome coupled to read-depth based copy number variation analysis in patients with inherited ataxias. Hum Mutat 2016; 37 (12) 1340-1353
• 12 Vona B, Müller T, Nanda I. , et al. Targeted next-generation sequencing of deafness genes in hearing-impaired individuals uncovers informative mutations. Genet Med 2014; 16 (12) 945-953
• 13 Scarlato M, Nuara A, Gerevini S. , et al. A new double-trouble phenotype: fascioscapulohumeral muscular dystrophy ameliorates hereditary spastic paraparesis due to spastin mutation. J Neurol 2015; 262 (02) 476-478