Clinical massively parallel sequencing for the diagnosis of myopathies

Gorokhova, Svetlana; Biancalana, Valérie; Lévy, Nicolas; Laporte, Jocelyn; Bartoli, Marc; Krahn, Martin

doi:10.1016/j.neurol.2015.02.019

Cited by 10 publications

(11 citation statements)

References 83 publications

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“…In terms of cost and time effectiveness, and several quality control parameters, targeted sequencing has been accepted by several large‐scale studies as the method‐of‐choice in the neuromuscular disease (NMD) diagnostics (Ankala et al., ; Biancalana & Laporte, ; Gorokhova et al., ; Savarese et al., ; Vasli et al., ). However, defining the optimal size of the gene panel remains the biggest challenge in targeted sequencing (Volk & Kubisch, ).…”

Section: Introductionmentioning

confidence: 99%

Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies

et al. 2018

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Spinal muscular atrophies (SMAs) are a heterogeneous group of disorders characterized by muscular atrophy, weakness, and hypotonia due to suspected lower motor neuron degeneration (LMND). In a large cohort of 3,465 individuals suspected with SMA submitted for SMN1 testing to our routine diagnostic laboratory, 48.8% carried a homozygous SMN1 deletion, 2.8% a subtle mutation, and an SMN1 deletion, whereas 48.4% remained undiagnosed. Recently, several other genes implicated in SMA/LMND have been reported. Despite several efforts to establish a diagnostic algorithm for non-5q-SMA (SMA without deletion or point mutations in SMN1 [5q13.2]), data from large-scale studies are not available. We tested the clinical utility of targeted sequencing in non-5q-SMA by developing two different gene panels. We first analyzed 30 individuals with a small panel including 62 genes associated with LMND using IonTorrent-AmpliSeq target enrichment. Then, additional 65 individuals were tested with a broader panel encompassing up to 479 genes implicated in neuromuscular diseases (NMDs) with Agilent-SureSelect target enrichment. The NMD panel provided a higher diagnostic yield (33%) than the restricted LMND panel (13%). Nondiagnosed cases were further subjected to exome or genome sequencing. Our experience supports the use of gene panels covering a broad disease spectrum for diseases that are highly heterogeneous and clinically difficult to differentiate.

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Section: Introductionmentioning

confidence: 99%

Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies

et al. 2018

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“…The sequencing reaction is properly done on isolated individual DNA molecules by de novo synthesis of the second strand. 7 The parallel sequencing of a huge number of short DNA fragments produces a corresponding huge number of "sequence reads." The overlapping reads are aligned by computer algorithms to the deposited reference genome sequence, thus reconstructing the desired parts of the patient's genome.…”

Section: Technical Aspects Of Massive Parallel Sequencingmentioning

confidence: 99%

“…The overlapping reads are aligned by computer algorithms to the deposited reference genome sequence, thus reconstructing the desired parts of the patient's genome. 7 Another specialized algorithm (the "variant caller") then searches for discrepancies between the patient's DNA and the reference sequence, thus providing a list of sequence positions where the two genomes differ (variant list). On average, the exomes of any two individuals differ by approximately 20,000 variants.…”

Section: Technical Aspects Of Massive Parallel Sequencingmentioning

confidence: 99%

“…In the early 2000s, the so-called next-generation sequencing (NGS) techniques have been developed allowing the massive parallel sequencing of large groups of genes (gene panels) or even a whole exome, that is, all of the approximately 20,000 coding genes of our genome. [4][5][6][7] More than 300 genes with implication in neuromuscular disorders are known, 5…”

Section: Introductionmentioning

confidence: 99%

“…The main advantage of the method is to obtain the desired genetic information in a short time at an acceptable prize. 7 On the other hand, finding the causative variation is a challenging matter of knowledge-based interpretation. The primary output of a gene panel analysis is a long list of sequence variants (¼ divergences from the consensus reference sequence).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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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.

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Guidelines for genetic testing of muscle and neuromuscular junction disorders

2021

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Despite recent advances in the understanding of inherited muscle and neuromuscular junction diseases, as well as the advent of a wide range of genetic tests, patients continue to face delays in diagnosis of sometimes treatable disorders. These guidelines outline an approach to genetic testing in such disorders. Initially, a patient's phenotype is evaluated to identify myopathies requiring directed testing, including myotonic dystrophies, facioscapulohumeral muscular dystrophy, oculopharyngeal muscular dystrophy, mitochondrial myopathies, dystrophinopathies, and oculopharyngodistal myopathy. Initial investigation in the remaining patients is generally a comprehensive gene panel by next-generation sequencing. Broad panels have a higher diagnostic yield and can be cost-effective. Due to extensive phenotypic overlap and treatment implications, genes responsible for congenital myasthenic syndromes should be included when evaluating myopathy patients. For patients whose initial genetic testing is negative or inconclusive, phenotypic re-evaluation is warranted, along with consideration of genes and variants not included initially, as well as their acquired mimickers.

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Clinical massively parallel sequencing for the diagnosis of myopathies

Cited by 10 publications

References 83 publications

Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies

Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies

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

Guidelines for genetic testing of muscle and neuromuscular junction disorders

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