scholarly journals Next-Generation Sequencing to Diagnose Muscular Dystrophy, Rhabdomyolysis, and HyperCKemia

2018 ◽  
Vol 45 (3) ◽  
pp. 262-268 ◽  
Author(s):  
Lily Wu ◽  
Lauren Brady ◽  
John Shoffner ◽  
Mark A. Tarnopolsky
Keyword(s):  
Next Generation Sequencing ◽  
Muscular Dystrophy ◽  
Muscle Weakness ◽  
Neuromuscular Disorders ◽  
Cost Effective ◽  
Muscle Disease ◽  
Muscle Pathology ◽  
Next Generation ◽  
Pathogenic Variants ◽  
Generation Sequencing

AbstractBackground:Neuromuscular disorders are a phenotypically and genotypically diverse group of diseases that can be difficult to diagnose accurately because of overlapping clinical features and nonspecific muscle pathology. Next-generation sequencing (NGS) is a high-throughput technology that can be used as a more time- and cost-effective tool for identifying molecular diagnoses for complex genetic conditions, such as neuromuscular disorders.Methods:One hundred and sixty-nine patients referred to a Canadian neuromuscular clinic for evaluation of possible muscle disease were screened with an NGS panel of muscular dystrophy–associated genes. Patients were categorized by the reason of referral (1) muscle weakness (n=135), (2) recurrent episodes of rhabdomyolysis (n=18), or (3) idiopathic hyperCKemia (n=16).Results:Pathogenic and likely pathogenic variants were identified in 36.09% of patients (61/169). The detection rate was 37.04% (50/135) in patients with muscle weakness, 33.33% (6/18) with rhabdomyolysis, and 31.25% (5/16) in those with idiopathic hyperCKemia.Conclusions:This study shows that NGS can be a useful tool in the molecular workup of patients seen in a neuromuscular clinic. Evaluating the utility of large panels of a muscle disease-specific NGS panel to investigate the genetic susceptibilities of rhabdomyolysis and/or idiopathic hyperCKemia is a relatively new field. Twenty-eight of the pathogenic and likely pathogenic variants reported here are novel and have not previously been associated with disease.

Just Expect It: Compound Heterozygous Variants of POMT1 in a Consanguineous Family—The Role of Next Generation Sequencing in Neuromuscular Disorders

2019 ◽  
Vol 51 (01) ◽  
pp. 072-075
Author(s):  
Maja von der Hagen ◽  
Lena-Luise Becker ◽  
Thomas F. Wienker ◽  
Martin Smitka ◽  
Luciana Musante ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Muscular Dystrophy ◽  
Neuromuscular Disorders ◽  
Brain Magnetic Resonance Imaging ◽  
Homozygosity Mapping ◽  
Compound Heterozygous ◽  
Homozygous Mutation ◽  
Next Generation ◽  
Generation Sequencing

AbstractMuscular dystrophy-dystroglycanopathies (MDDG) are a group of genetically heterogeneous autosomal recessive disorders characterized by hypoglycosylation of α-dystroglycan. Here, we report on two female patients from a consanguineous Lebanese family that presented in early infancy with generalized muscle hypotonia and primary microcephaly. Brain magnetic resonance imaging (MRI) showed different degrees of hypoplasia of the cerebellar vermis and hypoplasia of corpus callosum. Muscle biopsy analyses revealed a muscular dystrophy with reduced expression of α-dystroglycan and merosin in immunoblot analyses. Homozygosity mapping failed to elucidate the causal mutation due to the accepted notion that, in consanguineous families, homozygote mutations cause disease. However, by applying whole exome sequencing, we identified a novel compound heterozygous POMT1 mutation that segregates with the phenotype and is in line with the clinical presentation. This underscores that a less expected compound heterozygous instead of homozygous mutation in a consanguineous marriage results in a recessive disorder and highlights the growing role of next generation sequencing in neuromuscular disorder diagnostics.

scholarly journals Next-generation sequencing in the clinical genetic screening of patients with pheochromocytoma and paraganglioma

2013 ◽  
Vol 2 (2) ◽  
pp. 104-111 ◽  
Author(s):  
Joakim Crona ◽  
Alberto Delgado Verdugo ◽  
Dan Granberg ◽  
Staffan Welin ◽  
Peter Stålberg ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Screening ◽  
Bioinformatics Analysis ◽  
Cost Effective ◽  
Susceptibility Genes ◽  
Next Generation ◽  
Clinical Genetic ◽  
Cost Effective Method ◽  
Agilent Sureselect ◽  
Generation Sequencing

BackgroundRecent findings have shown that up to 60% of pheochromocytomas (PCCs) and paragangliomas (PGLs) are caused by germline or somatic mutations in one of the 11 hitherto known susceptibility genes: SDHA, SDHB, SDHC, SDHD, SDHAF2, VHL, HIF2A (EPAS1), RET, NF1, TMEM127 and MAX. This list of genes is constantly growing and the 11 genes together consist of 144 exons. A genetic screening test is extensively time consuming and expensive. Hence, we introduce next-generation sequencing (NGS) as a time-efficient and cost-effective alternative.MethodsTumour lesions from three patients with apparently sporadic PCC were subjected to whole exome sequencing utilizing Agilent Sureselect target enrichment system and Illumina Hi seq platform. Bioinformatics analysis was performed in-house using commercially available software. Variants in PCC and PGL susceptibility genes were identified.ResultsWe have identified 16 unique genetic variants in PCC susceptibility loci in three different PCC, spending less than a 30-min hands-on, in-house time. Two patients had one unique variant each that was classified as probably and possibly pathogenic: NF1 Arg304Ter and RET Tyr791Phe. The RET variant was verified by Sanger sequencing.ConclusionsNGS can serve as a fast and cost-effective method in the clinical genetic screening of PCC. The bioinformatics analysis may be performed without expert skills. We identified process optimization, characterization of unknown variants and determination of additive effects of multiple variants as key issues to be addressed by future studies.

scholarly journals Male Infertility Diagnosis: Improvement of Genetic Analysis Performance by the Introduction of Pre-Diagnostic Genes in a Next-Generation Sequencing Custom-Made Panel

2021 ◽  
Vol 11 ◽  
Author(s):  
Vincenza Precone ◽  
Rossella Cannarella ◽  
Stefano Paolacci ◽  
Gian Maria Busetto ◽  
Tommaso Beccari ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Male Infertility ◽  
Next Generation ◽  
Male Population ◽  
Pathogenic Variants ◽  
Custom Made ◽  
Number Of Genes ◽  
General Male Population ◽  
Generation Sequencing ◽  
Spermatogenic Failure

BackgroundInfertility affects about 7% of the general male population. The underlying cause of male infertility is undefined in about 50% of cases (idiopathic infertility). The number of genes involved in human spermatogenesis is over two thousand. Therefore, it is essential to analyze a large number of genes that may be involved in male infertility. This study aimed to test idiopathic male infertile patients negative for a validated panel of “diagnostic” genes, for a wide panel of genes that we have defined as “pre-diagnostic.”MethodsWe developed a next-generation sequencing (NGS) gene panel including 65 pre-diagnostic genes that were used in 12 patients who were negative to a diagnostic genetic test for male infertility disorders, including primary spermatogenic failure and central hypogonadism, consisting of 110 genes.ResultsAfter NGS sequencing, variants in pre-diagnostic genes were identified in 10/12 patients who were negative to a diagnostic test for primary spermatogenic failure (n = 9) or central hypogonadism (n = 1) due to mutations of single genes. Two pathogenic variants of DNAH5 and CFTR genes and three uncertain significance variants of DNAI1, DNAH11, and CCDC40 genes were found. Moreover, three variants with high impact were found in AMELY, CATSPER 2, and ADCY10 genes.ConclusionThis study suggests that searching for pre-diagnostic genes may be of relevance to find the cause of infertility in patients with apparently idiopathic primary spermatogenic failure due to mutations of single genes and central hypogonadism.

scholarly journals Next‐generation sequencing for the diagnosis of MYH9 ‐RD: Predicting pathogenic variants

2019 ◽  
Vol 41 (1) ◽  
pp. 277-290 ◽  
Author(s):  
Loredana Bury ◽  
Karyn Megy ◽  
Jonathan C. Stephens ◽  
Luigi Grassi ◽  
Daniel Greene ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Pathogenic Variants ◽  
Generation Sequencing

scholarly journals Targeted Next-Generation Sequencing in a Large Cohort of Genetically Undiagnosed Patients with Neuromuscular Disorders in Spain

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 539
Author(s):  
Lidia Gonzalez-Quereda ◽  
Maria Jose Rodriguez ◽  
Jordi Diaz-Manera ◽  
Jorge Alonso-Perez ◽  
Eduard Gallardo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Neuromuscular Disorders ◽  
Neuromuscular Disorder ◽  
Gene Panel ◽  
Muscular Dystrophies ◽  
Next Generation ◽  
Congenital Myasthenic Syndromes ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing ◽  
Myasthenic Syndromes

The term neuromuscular disorder (NMD) includes many genetic and acquired diseases and differential diagnosis can be challenging. Next-generation sequencing (NGS) is especially useful in this setting given the large number of possible candidate genes, the clinical, pathological, and genetic heterogeneity, the absence of an established genotype-phenotype correlation, and the exceptionally large size of some causative genes such as TTN, NEB and RYR1. We evaluated the diagnostic value of a custom targeted next-generation sequencing gene panel to study the mutational spectrum of a subset of NMD patients in Spain. In an NMD cohort of 207 patients with congenital myopathies, distal myopathies, congenital and adult-onset muscular dystrophies, and congenital myasthenic syndromes, we detected causative mutations in 102 patients (49.3%), involving 42 NMD-related genes. The most common causative genes, TTN and RYR1, accounted for almost 30% of cases. Thirty-two of the 207 patients (15.4%) carried variants of uncertain significance or had an unidentified second mutation to explain the genetic cause of the disease. In the remaining 73 patients (35.3%), no candidate variant was identified. In combination with patients’ clinical and myopathological data, the custom gene panel designed in our lab proved to be a powerful tool to diagnose patients with myopathies, muscular dystrophies and congenital myasthenic syndromes. Targeted NGS approaches enable a rapid and cost-effective analysis of NMD- related genes, offering reliable results in a short time and relegating invasive techniques to a second tier.

scholarly journals Validation of variants using cost effective highresolution melting (HRM) analysis predicted from target re-sequencing in Eucalyptus

2020 ◽  
Vol 79 (2) ◽  
pp. 105-113
Author(s):  
Abdul Bari Muneera Parveen ◽  
Divya Lakshmanan ◽  
Modhumita Ghosh Dasgupta
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Sequence Data ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Time Saving ◽  
Hrm Analysis ◽  
The Cost ◽  
Generation Sequencing

The advent of next-generation sequencing has facilitated large-scale discovery and mapping of genomic variants for high-throughput genotyping. Several research groups working in tree species are presently employing next generation sequencing (NGS) platforms for marker discovery, since it is a cost effective and time saving strategy. However, most trees lack a chromosome level genome map and validation of variants for downstream application becomes obligatory. The cost associated with identifying potential variants from the enormous amount of sequence data is a major limitation. In the present study, high resolution melting (HRM) analysis was optimized for rapid validation of single nucleotide polymorphisms (SNPs), insertions or deletions (InDels) and simple sequence repeats (SSRs) predicted from exome sequencing of parents and hybrids of Eucalyptus tereticornis Sm. ? Eucalyptus grandis Hill ex Maiden generated from controlled hybridization. The cost per data point was less than 0.5 USD, providing great flexibility in terms of cost and sensitivity, when compared to other validation methods. The sensitivity of this technology in variant detection can be extended to other applications including Bar-HRM for species authentication and TILLING for detection of mutants.

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