Targeted massively parallel sequencing and histological assessment of skeletal muscles for the molecular diagnosis of inherited muscle disorders

Nishikawa, Akio; Mitsuhashi, Satomi; Miyata, Naomasa; Nishino, Ichizo

doi:10.1136/jmedgenet-2016-104073

Cited by 53 publications

(33 citation statements)

References 42 publications

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“…However, the diagnostic rate remains 30% (depending on the diagnostic platform used) 11 , leaving a large population of Mendelian diseases unsolved.…”

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confidence: 99%

Robust detection of tandem repeat expansions from long DNA reads

Mitsuhashi

Mizuguchi

et al. 2018

Preprint

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Tandemly repeated sequences are highly mutable and variable features of genomes. Tandem repeat expansions are responsible for a growing list of human diseases, even though it is hard to determine tandem repeat sequences with current DNA sequencing technology. Recent long-read technologies are promising, because the DNA reads are often longer than the repetitive regions, but are hampered by high error rates. Here, we report robust detection of human repeat expansions from careful alignments of long (PacBio and nanopore) reads to a reference genome. Our method (tandem-genotypes) is robust to systematic sequencing errors, inexact repeats with fuzzy boundaries, and low sequencing coverage. By comparing to healthy controls, we can prioritize pathological expansions within the top 10 out of 700000 tandem repeats in the genome. This may help to elucidate the many genetic diseases whose causes remain unknown.

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“…However, the diagnostic rate remains 30% (depending on the diagnostic platform used) 11 , leaving a large population of Mendelian diseases unsolved.…”

mentioning

confidence: 99%

Robust detection of tandem repeat expansions from long DNA reads

Mitsuhashi

Mizuguchi

et al. 2018

Preprint

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“…One in-frame deletion (c.6513_6515delTGT) and one missense mutation (c.8654T>C, p.Leu2885Pro) might lead to partial protein expression. The c.2049_2050delAG and c.6513_6515delTGT mutations have previously been reported [ 27 ], while other mutations have not been reported before. None of the newly identified mutations were found in a scan of 100 normal individuals.…”

Section: Resultsmentioning

confidence: 99%

“…However, conclusively proving the pathogenic variant is the most difficult part after obtaining the NGS results, therefore, establishment of genotype-phenotype correlation is crucial in making the final diagnosis. Detailed clinical and pathological investigation remains the basis [ 22 , 27 , 29 ].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive target capture/next-generation sequencing as a second-tier diagnostic approach for congenital muscular dystrophy in Taiwan

Liang¹,

Tian²,

Yuo³

et al. 2017

PLoS ONE

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PurposeCongenital muscular dystrophy (CMD) is a heterogeneous disease entity. The detailed clinical manifestation and causative gene for each subgroup of CMD are quite variable. This study aims to analyze the phenotypes and genotypes of Taiwanese patients with CMD as the epidemiology of CMD varies among populations and has been scantly described in Asia.MethodsA total of 48 patients suspected to have CMD were screened and categorized by histochemistry and immunohistochemistry studies. Different genetic analyses, including next-generation sequencing (NGS), were selected, based on the clinical and pathological findings.ResultsWe identified 17 patients with sarcolemma-specific collagen VI deficiency (SSCD), 6 patients with merosin deficiency, two with reduced alpha-dystroglycan staining, and two with striking lymphocyte infiltration in addition to dystrophic change on muscle pathology. Fourteen in 15 patients with SSCD, were shown to have COL6A1, COL6A2 or COL6A3 mutations by NGS analysis; all showed marked distal hyperlaxity and normal intelligence but the overall severity was less than in previously reported patients from other populations. All six patients with merosin deficiency had mutations in LAMA2. They showed relatively uniform phenotype that were compatible with previous studies, except for higher proportion of mental retardation with epilepsy. With reduced alpha-dystroglycan staining, one patient was found to carry mutations in POMT1 while another patient carried mutations in TRAPPC11. LMNA mutations were found in the two patients with inflammatory change on muscle pathology. They were clinically characterized by neck flexion limitation and early joint contracture, but no cardiac problem had developed yet.ConclusionMuscle pathology remains helpful in guiding further molecular analyses by direct sequencing of certain genes or by target capture/NGS as a second-tier diagnostic tool, and is crucial for establishing the genotype-phenotype correlation. We also determined the frequencies of the different types of CMD in our cohort which is important for the development of a specific care system for each disease.

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“…Thus, dysferlinopathy is the most common LGMD subtype in the Chinese population, but the relative frequencies of sarcoglycanopathies and LGMD 2A differ between the southern and northern regions of China. Furthermore, although dysferlinopathy is also most frequent in Korean and Japanese populations, the frequencies of LGMD 2A, sarcoglycanopathies, and LGMD 1B vary among countries [ 32 , 45 ]. Therefore, the top 4 LGMD subtypes in East Asia include dysferlinopathy, LGMD 2A, and LGMD 1B, but the ranks of LGMD 2A and LGMD 1B differ between regions.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, the top 4 LGMD subtypes in East Asia include dysferlinopathy, LGMD 2A, and LGMD 1B, but the ranks of LGMD 2A and LGMD 1B differ between regions. The frequency of sarcoglycanopathies varies greatly among regions, and the top 4 LGMD subtypes in Korea did not include sarcoglycanopathies [ 16 , 32 , 44 , 45 ]. The reason for this phenomenon is not clear at present, which warrants further investigation.…”

Section: Discussionmentioning

confidence: 99%

The clinical spectrum and genetic variability of limb-girdle muscular dystrophy in a cohort of Chinese patients

Wang

Zhang

Li³

et al. 2018

Orphanet J Rare Dis

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BackgroundLimb-girdle muscular dystrophy (LGMD) is a commonly diagnosed hereditary muscular disorder, characterized by the progressive weakness of the limb-girdle muscles. Although the condition has been well-characterized, clinical and genetic heterogeneity can be observed in patients with LGMD. Here, we aimed to describe the clinical manifestations and genetic variability among a cohort of patients with LGMD in South China.ResultsWe analyzed the clinical information, muscle magnetic resonance imaging (MRI) findings, and genetic results obtained from 30 patients (24 families) with clinically suspected LGMD. In 24 probands, 38 variants were found in total, of which 18 were shown to be novel. Among the 30 patients, the most common subtypes were dysferlinopathy in eight (26.67%), sarcoglycanopathies in eight [26.67%; LGMD 2C in three (10.00%), LGMD 2D in three (10.00%), and LGMD 2F in two (6.67%)], LGMD 2A in seven (23.33%), followed by LGMD 1B in three (10.00%), LGMD 2I in three (10.00%), and early onset recessive Emery-Dreifuss-like phenotype without cardiomyopathy in one (3.33%). Furthermore, we also observed novel clinical presentations for LGMD 1B, 2F, and 2I patients with hypermobility of the joints in the upper limbs, a LGMD 2F patient with delayed language development, and other manifestations. Moreover, distinct distributions of fatty infiltration in patients with LGMD 2A, dysferlinopathy, and the early onset recessive Emery-Dreifuss-like phenotype without cardiomyopathy were also observed based on muscle MRI results.ConclusionsIn this study, we expanded the clinical spectrum and genetic variability found in patients with LGMD, which provided additional insights into genotype and phenotype correlations in this disease.Electronic supplementary materialThe online version of this article (10.1186/s13023-018-0859-6) contains supplementary material, which is available to authorized users.

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Targeted massively parallel sequencing and histological assessment of skeletal muscles for the molecular diagnosis of inherited muscle disorders

Abstract: Thus, we developed a high-throughput sequencing technique for diagnosing inherited muscle diseases. The use of this technique along with histological and protein analyses may be useful and cost-effective for screening mutations in patients with inherited skeletal muscle diseases.

Cited by 53 publications

References 42 publications

Robust detection of tandem repeat expansions from long DNA reads

Robust detection of tandem repeat expansions from long DNA reads

Comprehensive target capture/next-generation sequencing as a second-tier diagnostic approach for congenital muscular dystrophy in Taiwan

The clinical spectrum and genetic variability of limb-girdle muscular dystrophy in a cohort of Chinese patients

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