scholarly journals Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology

2016 ◽  
Vol 5 (1) ◽  
pp. 1-1 ◽  
Author(s):  
Samuel Cordey ◽  
Francisco Brito ◽  
Diem-Lan Vu ◽  
Lara Turin ◽  
Mary Kilowoko ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Respiratory Disease ◽  
Unknown Etiology ◽  
Next Generation ◽  
Acute Respiratory Disease ◽  
Tanzanian Child ◽  
Generation Sequencing

scholarly journals Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology

2016 ◽  
Vol 5 (1) ◽  
pp. 1-3 ◽  
Author(s):  
Samuel Cordey ◽  
Francisco Brito ◽  
Diem-Lan Vu ◽  
Lara Turin ◽  
Mary Kilowoko ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Respiratory Disease ◽  
Unknown Etiology ◽  
Next Generation ◽  
Acute Respiratory Disease ◽  
Tanzanian Child ◽  
Generation Sequencing

scholarly journals No Metagenomic Evidence of Causative Viral Pathogens in Postencephalitic Parkinsonism Following Encephalitis Lethargica

2021 ◽  
Vol 9 (8) ◽  
pp. 1716
Author(s):  
Dániel Cadar ◽  
Kurt A. Jellinger ◽  
Peter Riederer ◽  
Sabrina Strobel ◽  
Camelia-Maria Monoranu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Neuronal Loss ◽  
Unknown Etiology ◽  
Next Generation ◽  
Encephalitis Lethargica ◽  
Tissue Samples ◽  
Viral Pathogen ◽  
Postencephalitic Parkinsonism ◽  
Generation Sequencing ◽  
Post Infectious

Postencephalitic parkinsonism (PEP) is a disease of unknown etiology and pathophysiology following encephalitis lethargica (EL), an acute-onset polioencephalitis of cryptic cause in the 1920s. PEP is a tauopathy with multisystem neuronal loss and gliosis, clinically characterized by bradykinesia, rigidity, rest tremor, and oculogyric crises. Though a viral cause of EL is likely, past polymerase chain reaction-based investigations in the etiology of both PEP and EL were negative. PEP might be caused directly by an unknown viral pathogen or the consequence of a post-infectious immunopathology. The development of metagenomic next-generation sequencing in conjunction with bioinformatic techniques has generated a broad-range tool for the detection of unknown pathogens in the recent past. Retrospective identification and characterization of pathogens responsible for past infectious diseases can be successfully performed with formalin-fixed paraffin-embedded (FFPE) tissue samples. In this study, we analyzed 24 FFPE brain samples from six patients with PEP by unbiased metagenomic next-generation sequencing. Our results show that no evidence for the presence of a specific or putative (novel) viral pathogen was found, suggesting a likely post-infectious immune-mediated etiology of PEP.

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 Case Report: Diagnostic Value of Metagenomics Next Generation Sequencing in Intracranial Infection Caused by Mucor

2021 ◽  
Vol 8 ◽  
Author(s):  
YuChen Liu ◽  
Jun Zhang ◽  
Bing Han ◽  
LiJuan Du ◽  
ZhaoYang Shi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Case Reports ◽  
Relevant Literature ◽  
Traditional Culture ◽  
Unknown Etiology ◽  
Parasitic Infections ◽  
Serological Testing ◽  
Next Generation ◽  
Intracranial Infection ◽  
Generation Sequencing

mNGS(metagenomics Next Generation Sequencing), as a novel culture-independent approach, demonstrated the capability of rapid, sensitive, and accurate pathogen identification. At present, there have been many case reports about the use of mNGS to assist in the diagnosis of bacterial, fungal, viral and parasitic infections and to guide clinicians to determine appropriate treatment. However, the clinical understanding of this technique is not comprehensive, and the experience of using it is relatively limited. We reported a 53-year-old man who was admitted to hospital with a high fever and headache. His inflammatory biomarkers were markedly elevated. Based on the clinical presentation, He was initially diagnosed as having an intracranial infection of unknown etiology and received empirical antibiotics and systemic supportive treatment. But these did not relieve his symptoms. Both the blood and CSF specimens were examined using traditional culture, serological testing, and mNGS. Traditional culture and serological testing produced negative results, while the mNGS revealed the presence of a potential pathogen, mucor, in the CSF specimen. Then targeted antifungal treatment was selected quickly and his temperature gradually returned to normal. Thus, we report the case in which mNGS was an auxiliary method to diagnose mucormycosis, and discuss this case in combination with relevant literature, in order to improve the clinical cognition of this technology.

scholarly journals Next Generation Sequencing in Pediatric Epilepsy Using Customized Panels: Size Matters

2020 ◽  
Author(s):  
Eva-Katharina Willimsky ◽  
Anna Munzig ◽  
Karin Mayer ◽  
Saskia Biskup ◽  
Angela Abicht ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diagnostic Yield ◽  
Unknown Etiology ◽  
Pediatric Epilepsy ◽  
Next Generation ◽  
Large Panels ◽  
Pathogenic Variants ◽  
Gene Panels ◽  
Patients With Epilepsy ◽  
Generation Sequencing

Abstract Introduction Next generation sequencing (NGS) with customized gene panels is a helpful tool to identify monogenic epilepsy syndromes. The number of genes tested within a customized panel may vary greatly. The aim of the present study was to compare the diagnostic yield of small (<25 kb) and large (>25 kb) customized epilepsy panels. Methods This retrospective cohort study investigated data of 190 patients of 18 years or younger, with the diagnosis of an epilepsy of unknown etiology who underwent NGS using customized gene panels. Small (<25 kb) and large (>25 kb) panels were compared regarding the distribution of benign/likely benign and pathogenic/likely pathogenic variants and variants of unclear significance. In addition, differences of the diagnostic yield with respect to epilepsy severity, i.e., developmental and epileptic encephalopathy [DEE] vs. non-DEE, were analyzed. Results The diagnostic yield defined as pathogenic or likely pathogenic variants in large panels was significantly increased (29% [n = 14/48] vs. 13% [n = 18/142], p = 0.0198) compared with smaller panels. In non-DEE patients the increase of the diagnostic yield in large panels was significant(35% n = 6/17 vs. 13% n = 12/94, p = 0.0378), which was not true for DEE patients. Discussion This study indicates that large panels are superior for pediatric patients with epilepsy forms without encephalopathy (non-DEE). For patients suffering from DEE small panels of a maximum of 10 genes seem to be sufficient. The proportion of unclear findings increases with rising panel sizes. Conclusion Customized epilepsy panels of >25 kb compared with smaller panels show a significant higher diagnostic yield in patients with epilepsy especially in non-DEE patients.

Improved molecular diagnosis of patients with neonatal diabetes using a combined next-generation sequencing and MS-MLPA approach

2016 ◽  
Vol 29 (5) ◽  
Author(s):  
Gorka Alkorta-Aranburu ◽  
Madina Sukhanova ◽  
David Carmody ◽  
Trevor Hoffman ◽  
Latrice Wysinger ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnosis ◽  
Neonatal Diabetes ◽  
Unknown Etiology ◽  
Chromosome 6 ◽  
Next Generation ◽  
Transient Neonatal Diabetes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Parental Inheritance

Abstract: We evaluated a methylation-specific multiplex-ligation-dependent probe amplification (MS-MLPA) assay for the molecular diagnosis of transient neonatal diabetes mellitus (TNDM) caused by 6q24 abnormalities and assessed the clinical utility of using this assay in combination with next generation sequencing (NGS) analysis for diagnosing patients with neonatal diabetes (NDM).: We performed MS-MLPA in 18 control samples and 42 retrospective NDM cases with normal bi-parental inheritance of chromosome 6. Next, we evaluated 22 prospective patients by combining NGS analysis of 11 NDM genes and the MS-MLPA assay.: 6q24 aberrations were identified in all controls and in 19% of patients with normal bi-parental inheritance of chromosome 6. The MS-MLPA/NGS combined approach identified a genetic cause in ~64% of patients with NDM of unknown etiology.MS-MLPA is a reliable method to identify all known 6q24 abnormalities and comprehensive testing of all causes reveals a causal mutation in ~64% of patients.

scholarly journals Diagnostic Yield of Next-Generation Sequencing in Patients With Chronic Kidney Disease of Unknown Etiology

2019 ◽  
Vol 10 ◽  
Author(s):  
Amber de Haan ◽  
Mark Eijgelsheim ◽  
Liffert Vogt ◽  
Nine V. A. M. Knoers ◽  
Martin H. de Borst
Keyword(s):  
Chronic Kidney Disease ◽  
Next Generation Sequencing ◽  
Kidney Disease ◽  
Diagnostic Yield ◽  
Unknown Etiology ◽  
Next Generation ◽  
Generation Sequencing

Cerebrospinal Fluid Analysis for Viruses by Metagenomic Next-Generation Sequencing in Pediatric Encephalitis: Not Yet Ready for Prime Time?

2020 ◽  
pp. 088307382097223
Author(s):  
Guliz Erdem ◽  
Irina Kaptsan ◽  
Himanshu Sharma ◽  
Arvind Kumar ◽  
Shawn C. Aylward ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Cerebrospinal Fluid ◽  
Nervous System ◽  
Next Generation Sequencing ◽  
Intracranial Hypertension ◽  
Immunocompromised Patient ◽  
Unknown Etiology ◽  
Next Generation ◽  
Viral Pathogens ◽  
Generation Sequencing

Background: Metagenomic next-generation sequencing offers an unbiased approach to identifying viral pathogens in cerebrospinal fluid of patients with meningoencephalitis of unknown etiology. Methods: In an 11-month case series, we investigated the use of cerebrospinal fluid metagenomic next-generation sequencing to diagnose viral infections among pediatric hospitalized patients presenting with encephalitis or meningoencephalitis of unknown etiology. Cerebrospinal fluid from patients with known enterovirus meningitis were included as positive controls. Cerebrospinal fluid from patients with primary intracranial hypertension were included to serve as controls without known infections. Results: Cerebrospinal fluid metagenomic next-generation sequencing was performed for 37 patients. Among 27 patients with encephalitis or meningoencephalitis, 4 were later diagnosed with viral encephalitis, 6 had non–central nervous system infections with central nervous system manifestations, 6 had no positive diagnostic tests, and 11 were found to have a noninfectious diagnosis. Metagenomic next-generation sequencing identified West Nile virus (WNV) in the cerebrospinal fluid of 1 immunocompromised patient. Among the 4 patients with known enterovirus meningitis, metagenomic next-generation sequencing correctly identified enteroviruses and characterized the viral genotype. No viral sequences were detected in the cerebrospinal fluid of patients with primary intracranial hypertension. Metagenomic next-generation sequencing also identified sequences of nonpathogenic torque Teno virus in cerebrospinal fluid specimens from 13 patients. Conclusions: Our results showed viral detection by cerebrospinal fluid metagenomic next-generation sequencing only in 1 immunocompromised patient and did not offer a diagnostic advantage over conventional testing. Viral phylogenetic characterization by metagenomic next-generation sequencing could be used in epidemiologic investigations of some viral pathogens, such as enteroviruses. The finding of torque Teno viruses in cerebrospinal fluid by metagenomic next-generation sequencing is of unknown significance but may merit further exploration for a possible association with noninfectious central nervous system disorders.

Next-Generation Sequencing

2012 ◽  
Vol 42 (9) ◽  
pp. 8
Author(s):  
PETER HULICK
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing
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