scholarly journals 112 Axonal polyneuropathy with onset in young adulthood due to TUBB3 mutation

2019 ◽  
Vol 90 (e7) ◽  
pp. A36.2-A36
Author(s):  
Po Sheng Yang ◽  
Kimberley K Forrest ◽  
Ian B Wilson
Keyword(s):  
Next Generation Sequencing ◽  
Axonal Neuropathy ◽  
Extraocular Muscles ◽  
Diagnostic Process ◽  
List Type ◽  
Next Generation ◽  
Sensorimotor Polyneuropathy ◽  
Axonal Polyneuropathy ◽  
Congenital Fibrosis ◽  
Generation Sequencing

IntroductionThe TUBB3 gene encodes the protein Beta-tubulin isotype III, a component of the microtubule cytoskeleton. Mutations in this gene have been associated with axonal polyneuropathy, however usually associated with congenital fibrosis of the extraocular muscles (CFOEM) and other abnormalities of cerebral development.1 2 We report a case of isolated neuropathy associated with a TUBB3 mutation.MethodsCase report - clinical information and next generation sequencing results were obtained.ResultsA 64 year old man presented with a severe, progressive, length dependent sensorimotor polyneuropathy which commenced in his late twenties. There was no clinical involvement of the extraocular muscles and cognition was normal. Family history was limited, but there were no other members affected.The patient had previously been extensively investigated including sural nerve biopsy, which confirmed axonal neuropathy without a specific diagnosis. Intravenous immunoglobulins and steroids had been trialled without benefit.A neuromuscular gene panel utilising next generation sequencing was performed and demonstrated heterozygosity for a variant of the TUBB3 gene (D417N substitution).Case series describing TUBB3 mutations show a large heterogeneity in phenotypic expression depending on the amino acid substitution.2–4 There is also heterogeneity in patients with D417N mutations, although a small number have been reported to develop a polyneuropathy without CFOEM1.ConclusionsThis case strengthens previous reports that TUBB3 mutation can be associated with a pure, axonal, sensorimotor polyneuropathy and highlights the use of next generation sequencing in streamlining the diagnostic process.ReferenceTischfield M, et al. Human TUBB3 mutations perturb microtubule dynamics, kinesin interactions, and axon guidance. Cell 2010;140(1):pp.74–87.Ncbi.nlm.nih.gov. (2019). Congenital fibrosis of the extraocular muscles - Conditions - GTR - NCBI. [online] Available at: https://www.ncbi.nlm.nih.gov/gtr/conditions/CN043677/ [Accessed 14 Feb. 2019].Omim.org. (2019). OMIM Entry - * 602661 - TUBULIN, BETA-3; TUBB3. [online] Available at: https://www.omim.org/entry/602661 [Accessed 14 Feb. 2019].Krupa, K. and Bekiesinska-Figatowska, M. (2013). Congenital and Acquired Abnormalities of the Corpus Callosum: A Pictorial Essay. BioMed Research International, 2013, pp.1–14.

scholarly journals RNA Analysis as a Tool to Determine Clinically Relevant Gene Fusions and Splice Variants

2018 ◽  
Vol 142 (4) ◽  
pp. 474-479 ◽  
Author(s):  
Cristina Teixidó ◽  
Ana Giménez-Capitán ◽  
Miguel Ángel Molina-Vila ◽  
Vicente Peg ◽  
Niki Karachaliou ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Splice Variants ◽  
Treatment Options ◽  
Diagnostic Process ◽  
Gene Fusions ◽  
Next Generation ◽  
Liquid Biopsies ◽  
Rna Analysis ◽  
Generation Sequencing

Context.— Technologic advances have contributed to the increasing relevance of RNA analysis in clinical oncology practice. The different genetic aberrations that can be screened with RNA include gene fusions and splice variants. Validated methods of identifying these alterations include fluorescence in situ hybridization, immunohistochemistry, reverse transcription–polymerase chain reaction, and next-generation sequencing, which can provide physicians valuable information on disease and treatment of cancer patients. Objective.— To discuss the standard techniques available and new approaches for the identification of gene fusions and splice variants in cancer, focusing on RNA analysis and how analytic methods have evolved in both tissue and liquid biopsies. Data Sources.— This is a narrative review based on PubMed searches and the authors' own experiences. Conclusions.— Reliable RNA-based testing in tissue and liquid biopsies can inform the diagnostic process and guide physicians toward the best treatment options. Next-generation sequencing methodologies permit simultaneous assessment of molecular alterations and increase the number of treatment options available for cancer patients.

The utility of next-generation sequencing technologies in diagnosis of Mendelian mitochondrial diseases and reflections on clinical spectrum

2021 ◽  
Vol 34 (4) ◽  
pp. 417-430
Author(s):  
Melis Kose ◽  
Esra Isik ◽  
Ayça Aykut ◽  
Asude Durmaz ◽  
Engin Kose ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Exome Sequencing ◽  
Diagnostic Process ◽  
Unknown Etiology ◽  
Next Generation ◽  
Related Gene ◽  
Targeted Exome Sequencing ◽  
Novel Variants ◽  
Gene Defects ◽  
Generation Sequencing

Abstract Objectives Diagnostic process of mitochondrial disorders (MD) is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next-Generation Sequencing (NGS) technology offers a high-throughput platform for nuclear MD. Methods We included 59 of 72 patients that undergone WES and targeted exome sequencing panel suspected to have potential PMDs. Patients who were included in the analysis considering the possible PMD were reviewed retrospectively and scored according to the Mitochondrial Disease Criteria Scale. Results Sixty-one percent of the patients were diagnosed with whole-exome sequencing (WES) (36/59) and 15% with targeted exome sequencing (TES) (9/59). Patients with MD-related gene defects were included in the mito group, patients without MD-related gene defects were included in the nonmito group, and patients in whom no etiological cause could be identified were included in the unknown etiology group. In 11 out of 36 patients diagnosed with WES, a TES panel was applied prior to WES. In 47 probands in 39 genes (SURF1, SDHAF1, MTO1, FBXL4, SLC25A12, GLRX5, C19oRF12, NDUFAF6, DARS2, BOLA3, SLC19A3, SCO1, HIBCH, PDHA1, PDHAX, PC, ETFA, TRMU, TUFM, NDUFS6, WWOX, UBCD TREX1, ATL1, VAC14, GFAP, PLA2G6, TPRKB, ATP8A2, PEX13, IGHMBP2, LAMB2, LPIN1, GFPT1, CLN5, DOLK) (20 mito group, 19 nonmito group) 59 variants (31 mito group, 18 nonmito group) were detected. Seven novel variants in the mito group (SLC25A12, GLRX5, DARS2, SCO1, PC, ETFA, NDUFS6), nine novel variants in the nonmito group (IVD, GCDH, COG4, VAC14, GFAP, PLA2G6, ATP8A2, PEX13, LPIN1) were detected. Conclusions We explored the feasibility of identifying pathogenic alleles using WES and TES in MD. Our results show that WES is the primary method of choice in the diagnosis of MD until at least all genes responsible for PMD are found and are highly effective in facilitating the diagnosis process.

scholarly journals Population genomic SNPs from epigenetic RADs: gaining genetic and epigenetic data from a single established next-generation sequencing approach

2019 ◽  
Author(s):  
M. Crotti ◽  
C.E. Adams ◽  
K.R. Elmer
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
List Type ◽  
Summary Statistics ◽  
Next Generation ◽  
Population Genomic ◽  
Genome Wide ◽  
Generation Sequencing

SummaryEpigenetics is increasingly recognised as an important molecular mechanism underlying phenotypic variation. To study DNA methylation in ecological and evolutionary contexts, epiRADseq is a cost-effective next-generation sequencing technique based on reduced representation sequencing of genomic regions surrounding non-/methylated sites. EpiRADseq for genome-wide methylation abundance and ddRADseq for genome-wide SNP genotyping follow very similar library and sequencing protocols, but to date these two types of dataset have been handled separately. Here we test the performance of using epiRADseq data to generate SNPs for population genomic analyses.We tested the robustness of using epiRADseq data for population genomics with two independent datasets: a newly generated single-end dataset for the European whitefish Coregonus lavaretus, and a re-analysis of publicly available, previously published paired-end data on corals. Using standard bioinformatic pipelines with a reference genome and without (i.e. de novo catalogue loci), we compared the number of SNPs retained, population genetic summary statistics, and population genetic structure between data drawn from ddRADseq and epiRADseq library preparations.We find that SNPs drawn from epiRADseq are similar in number to those drawn from ddRADseq, with a 55-83% of SNPs being identified by both methods. Genotyping error rate was <5% in both approaches. For summary statistics such as heterozygosity and nucleotide diversity, there is a strong correlation between methods (Spearman’s rho > 0.88). Furthermore, identical patterns of population genetic structure were recovered using SNPs from epiRADseq and ddRADseq approaches.We show that SNPs obtained from epiRADseq are highly similar to those from ddRADseq and are equivalent for estimating genetic diversity and population structure. This finding is particularly relevant to researchers interested in genetics and epigenetics on the same individuals because using a single epigenomic approach to generate two datasets greatly reduces the time and financial costs compared to using these techniques separately. It also efficiently enables correction of epigenetic estimates with population genetic data. Many studies will benefit from a combinatorial approach with genetic and epigenetic markers and this demonstrates a single, efficient method to do so.

scholarly journals QTLseqr: An R package for bulk segregant analysis with next-generation sequencing

2017 ◽  
Author(s):  
Ben N. Mansfeld ◽  
Rebecca Grumet
Keyword(s):  
Next Generation Sequencing ◽  
Bulk Segregant Analysis ◽  
Statistical Significance ◽  
Simulation Method ◽  
R Package ◽  
List Type ◽  
Next Generation ◽  
Snp Data ◽  
R Packages ◽  
Generation Sequencing

1AbstractNext Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G’. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr, can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G’ values, and log10(p-values), enabling identification and plotting of QTL. The source code is available at https://github.com/bmansfeld/QTLseqr.Core ideasAn R package that performs Next Generation Sequencing Bulk Segregant Analysis was developedTwo methods for analysis are provided: QTL-seq and G’The QTLseqr package is quick and produces publication quality figures and tables

scholarly journals Targeted next-generation sequencing panels in the diagnosis of Charcot-Marie-Tooth disease

Neurology ◽  
2019 ◽  
Vol 94 (1) ◽  
pp. e51-e61 ◽  
Author(s):  
Andrea Cortese ◽  
Janel E. Wilcox ◽  
James M. Polke ◽  
Roy Poh ◽  
Mariola Skorupinska ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnosis ◽  
Positive Family History ◽  
Diagnostic Process ◽  
Next Generation ◽  
Charcot Marie Tooth ◽  
Targeted Next Generation Sequencing ◽  
Charcot Marie Tooth Disease ◽  
Generation Sequencing ◽  
Tooth Disease

ObjectiveTo investigate the effectiveness of targeted next-generation sequencing (NGS) panels in achieving a molecular diagnosis in Charcot-Marie-Tooth disease (CMT) and related disorders in a clinical setting.MethodsWe prospectively enrolled 220 patients from 2 tertiary referral centers, one in London, United Kingdom (n = 120), and one in Iowa (n = 100), in whom a targeted CMT NGS panel had been requested as a diagnostic test. PMP22 duplication/deletion was previously excluded in demyelinating cases. We reviewed the genetic and clinical data upon completion of the diagnostic process.ResultsAfter targeted NGS sequencing, a definite molecular diagnosis, defined as a pathogenic or likely pathogenic variant, was reached in 30% of cases (n = 67). The diagnostic rate was similar in London (32%) and Iowa (29%). Variants of unknown significance were found in an additional 33% of cases. Mutations in GJB1, MFN2, and MPZ accounted for 39% of cases that received genetic confirmation, while the remainder of positive cases had mutations in diverse genes, including SH3TC2, GDAP1, IGHMBP2, LRSAM1, FDG4, and GARS, and another 12 less common genes. Copy number changes in PMP22, MPZ, MFN2, SH3TC2, and FDG4 were also accurately detected. A definite genetic diagnosis was more likely in cases with an early onset, a positive family history of neuropathy or consanguinity, and a demyelinating neuropathy.ConclusionsNGS panels are effective tools in the diagnosis of CMT, leading to genetic confirmation in one-third of cases negative for PMP22 duplication/deletion, thus highlighting how rarer and previously undiagnosed subtypes represent a relevant part of the genetic landscape of CMT.

scholarly journals Pheochromocytoma due to a novel SDHD variant presenting as unilateral visual loss

2021 ◽  
Vol 2021 ◽  
Author(s):  
Clare Miller ◽  
Agnieszka Pazderska ◽  
John Reynolds ◽  
Patricia Gou ◽  
Barbara Dunne ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Organ Damage ◽  
Secondary Hypertension ◽  
Cystoid Macular Oedema ◽  
List Type ◽  
Next Generation ◽  
Novel Variants ◽  
High Heritability ◽  
Learning Points ◽  
Generation Sequencing

Summary A 53-year-old female presented to a tertiary ophthalmology referral centre complaining of unilateral painless loss of vision. Subsequent assessment revealed malignant hypertension causing right-sided cystoid macular oedema. During the course of secondary hypertension workup, she was diagnosed with a 7.8 cm phaeochromocytoma which was resected. Testing for a panel of all predisposing phaeochromocytoma-causing variants using next-generation sequencing resulted in the diagnosis of a novel SDHD variant. Learning points Screening for secondary causes of hypertension is indicated when there is evidence of hypertension-mediated end-organ damage (1). Testing for a predisposing variant should be considered in all patients with phaeochromocytoma or paraganglioma due to the high heritability rate and prevalence of somatic variants (2, 3, 4). Novel variants are commonly uncovered in the Succinate Dehydrogenase (SDH) subunit; proving pathogenicity is a complex, time-consuming process and one challenge of next-generation sequencing (3). SDHB immunohistochemistry as a tool for demonstrating pathogenicity is associated with reduced sensitivity when assessing SDHD variants (5, 6).

scholarly journals Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Kidney Disease-Related Genes in Patients with Diabetic Kidney Disease

2020 ◽  
Author(s):  
Jose Lazaro-Guevara ◽  
Julio Fierro Morales ◽  
A. Hunter Wright ◽  
River Gunville ◽  
Scott G. Frodsham ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Kidney Disease ◽  
Diabetic Kidney Disease ◽  
List Type ◽  
Next Generation ◽  
Diabetic Kidney ◽  
Pathogenic Variants ◽  
Patients With Diabetes ◽  
Disease Related Genes ◽  
Generation Sequencing

AbstractDiabetes is the most common cause of chronic kidney disease (CKD). For patients with diabetes and CKD, the underlying cause of their kidney disease is often assumed to be a consequence of their diabetes. Without histopathological confirmation, however, the underlying cause of their kidney disease is unclear. Recent studies have shown that next-generation sequencing (NGS) provides a promising avenue toward uncovering and establishing precise genetic diagnoses in various forms of kidney disease. Here, we set out to investigate the genetic basis of disease in non-diabetic kidney disease (NDKD) and diabetic kidney disease (DKD) patients by performing targeted NGS using a custom panel comprised of 345 kidney disease-related genes. Our analysis identified rare diagnostic variants that were consistent with the clinical diagnosis of 19% of the NDKD patients included in this study. Similarly, 22% of DKD patients were found to carry rare pathogenic/likely pathogenic variants in kidney disease-related genes included on our panel. Genetic variants suggestive of NDKD were detected in 3% of the diabetic patients included in this study. Our findings suggest that rare variants in kidney disease-related genes in the context of diabetic pathophysiology may play a role in the pathogenesis of kidney disease in patients with diabetes.Key MessagesWhat is already known about this subject? For patients with diabetes and chronic kidney disease, the underlying cause of their kidney disease is often assumed to be a consequence of their diabetes; without histopathological confirmation, however, the underlying cause of their kidney disease is unclear.Next-generation sequencing (NGS) provides a promising avenue toward uncovering and establishing precise genetic diagnoses in various forms of kidney disease.What are the new findings? Using targeted NGS and a custom panel comprised of 345 kidney disease-related genes, we found that 22% of diabetic kidney disease patients were found to carry rare pathogenic/likely pathogenic variants in kidney disease-related genes included on our panel.Genetic variants suggestive of non-diabetic kidney disease were detected in 3% of the diabetic patients included in this study.How might these results change the focus of research or clinical practice? Our findings suggest that rare variants in kidney disease-related genes in the context of diabetic pathophysiology may play a role in the pathogenesis of kidney disease in patients with diabetes.Importantly, improved understanding of the underlying disease process in diabetic kidney disease could have major implications in terms of patient care and monitoring as well as for research studies in this field.

scholarly journals Extremely fast and incredibly close: co-transcriptional splicing in budding yeast

2016 ◽  
Author(s):  
Edward W.J. Wallace ◽  
Jean D. Beggs
Keyword(s):  
Next Generation Sequencing ◽  
Ribosomal Protein ◽  
Rna Polymerase Ii ◽  
Rna Processing ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Budding Yeast ◽  
List Type ◽  
Next Generation ◽  
Generation Sequencing

AbstractRNA splicing, an essential part of eukaryotic pre-messenger RNA processing, can be simultaneous with transcription by RNA polymerase II. Here, we compare and review independent next-generation sequencing methods that quantify co-transcriptional splicing in budding yeast. Splicing in yeast is fast, taking place within seconds of intron transcription, while polymerase is within a few dozens of nucleotides of the 3’ splice site. Ribosomal protein mRNAs are spliced particularly fast and co-transcriptionally. Intron-mediated regulation of some genes is also likely to be co-transcriptional. We suggest that intermediates of the splicing reaction, missing from current datasets, may hold key information about splicing kinetics.TrendsIndependent next-generation sequencing methods quantify co-transcriptional splicing in budding yeastRibosomal protein mRNAs are spliced particularly fast and co-transcriptionallyIntron-mediated regulation of DBP2 and RPS9A is likely co-transcriptionalSplicing intermediates, missing from current datasets, may hold key information

scholarly journals Comparison Of Multi-locus Sequence Typing software For next generation sequencing data

2017 ◽  
Author(s):  
Andrew J. Page ◽  
Nabil-Fareed Alikhan ◽  
Heather A. Carleton ◽  
Torsten Seemann ◽  
Jacqueline A. Keane ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Diagnostics ◽  
Multi Locus Sequence Typing ◽  
Next Generation Sequencing Data ◽  
List Type ◽  
Next Generation ◽  
Sequencing Data ◽  
Software Applications ◽  
Link Type ◽  
Generation Sequencing

ABSTRACTMulti-locus sequence typing (MLST) is a widely used method for categorising bacteria. Increasingly MLST is being performed using next generation sequencing data by reference labs and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have compared six of these applications against real and simulated data and present results on: 1. the accuracy of each method against traditional typing methods, 2. the performance on real outbreak datasets, 3. in the impact of contamination and varying depth of coverage, and 4. the computational resource requirements.DATA SUMMARYSimulated reads for datasets testing coverage and mixed samples have been deposited in Figshare; DOI:https://doi.org/10.6084/m9.figshare.4602301.vlOutbreak databases are available from Github; url -https://github.com/WGS-standards-and-analysis/datasetsDocker containers used to run each of the applications are available from Github; url –https://tinyurl.com/z7ks2ftAccession numbers for the data used in this paper are available in the Supplementary material.We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ☒IMPACT STATEMENTSequence typing is rapidly transitioning from traditional sequencing methods to using whole genome sequencing. A number ofin silicoprediction methods have been developed on anad hocbasis and aim to replicate Multi-locus sequence typing (MLST). This is the first study to comprehensively evaluate multiple MLST software applications on real validated datasets and on common simulated difficult cases. It will give researchers a clearer understanding of the accuracy, limitations and computational performance of the methods they use, and will assist future researchers to choose the most appropriate method for their experimental goals.

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