scholarly journals Application of Next Generation Sequencing Genetic Studies of Urea Cycle Disorders

2021 ◽  
Vol 37 (2) ◽  
Author(s):  
Nguyen Thi Thu Huong ◽  
Nguyen Thi Kim Lien ◽  
Nguyen Huy Hoang
Keyword(s):  
Next Generation Sequencing ◽  
Urea Cycle ◽  
Rapid Development ◽  
Disease Diagnosis ◽  
Transport Systems ◽  
Future Research ◽  
Next Generation ◽  
Carbamoyl Phosphate ◽  
Genetic Studies ◽  
Generation Sequencing

Urea cycle disorder is a group of rare, inherited metabolic disorders in the pathway transforming ammonia to urea. The mutations in genes coding for 6 enzymes that are participated including carbamoyl phosphate synthase I (CPSI), ornithine transcarbamylase (OTC), argininosuccinate synthase (ASS1), argininosuccinate lyase (ASL), arginase (ARG1), and N-acetyl glutamate synthase (NAGS), and 2 transport systems ((ornithine translocase (ONT1), citrin)) in the urea cycle are responsible for ammonia accumulation in the blood. Hyperammonemia is the cause of severe neurological symptoms and even death. In almost all cases, clinical examinations and biochemical experiments are necessary, but insufficient information for an accurate diagnosis. Mutation analysis is an effective method to confirm the diagnosis and could be the basis for genetic counseling. The rapid development and widely using of next generation sequencing (NGS) have brought incredible advances in molecular diagnosis of genetic diseases in general. In this article, we systematize the UCD genetic studies applying NGS method, thereby providing a basis for not only disease diagnosis but also future research

The applications of next-generation sequencing (NGS) in drug development for cancer therapy

2020 ◽  
Vol 16 ◽  
Author(s):  
Pelin Telkoparan-Akillilar ◽  
Dilek Cevik
Keyword(s):  
Next Generation Sequencing ◽  
Drug Discovery ◽  
Cancer Therapy ◽  
Target Identification ◽  
Rapid Development ◽  
Next Generation ◽  
Biomedical Sciences ◽  
Dna And Rna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Background: Numerous sequencing techniques have been progressed since the 1960s with the rapid development of molecular biology studies focusing on DNA and RNA. Methods: a great number of articles, book chapters, websites are reviewed, and the studies covering NGS history, technology and applications to cancer therapy are included in the present article. Results: High throughput next-generation sequencing (NGS) technologies offer many advantages over classical Sanger sequencing with decreasing cost per base and increasing sequencing efficiency. NGS technologies are combined with bioinformatics software to sequence genomes to be used in diagnostics, transcriptomics, epidemiologic and clinical trials in biomedical sciences. The NGS technology has also been successfully used in drug discovery for the treatment of different cancer types. Conclusion: This review focuses on current and potential applications of NGS in various stages of drug discovery process, from target identification through to personalized medicine.

scholarly journals Next-Generation Sequencing in Human Genetic Studies: Genome Technologies and Applications to Human Genetic Studies

2018 ◽  
Vol 83 (3) ◽  
pp. 105-106
Author(s):  
Junwen Wang ◽  
Kai Wang ◽  
Xiaoming Liu ◽  
Pak Sham ◽  
Zhongming Zhao
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Genetic Studies ◽  
Generation Sequencing

Balamuthia mandrillaris-Related Primary Amoebic Encephalitis in China Diagnosed by Next Generation Sequencing and a Review of the Literature

2019 ◽  
Author(s):  
Yinan Yang ◽  
Xiaobin Hu ◽  
Li Min ◽  
Xiangyu Dong ◽  
Yuanlin Guan
Keyword(s):  
Next Generation Sequencing ◽  
Inflammatory Diseases ◽  
Clinical Manifestations ◽  
Infectious Agent ◽  
Disease Diagnosis ◽  
Rapid Identification ◽  
Next Generation ◽  
Balamuthia Mandrillaris ◽  
Granulomatous Amoebic Encephalitis ◽  
Generation Sequencing

Abstract Background Encephalitis is caused by infection, immune mediated diseases, or primary inflammatory diseases. Of all the causative infectious pathogens, 90% are viruses or bacteria. Granulomatous amoebic encephalitis (GAE), caused by Balamuthia mandrillaris, is a rare but life-threatening disease. Diagnosis and therapy are frequently delayed due to the lack of specific clinical manifestations. Method A healthy 2 year old Chinese male patient initially presented with a nearly 2 month history of irregular fever. We present this case of granulomatous amoebic encephalitis caused by B. mandrillaris. Next generation sequencing of the patient’s cerebrospinal fluid (CSF) was performed to identify an infectious agent. Result The results of next generation sequencing of the CSF showed that most of the mapped reads belonged to Balamuthia mandrillaris. Conclusion Next generation sequencing (NGS) is an unbiased and rapid diagnostic tool. The NGS method can be used for the rapid identification of causative pathogens. The NGS method should be widely applied in clinical practice and help clinicians provide direction for the diagnosis of diseases, especially for rare and difficult cases.

scholarly journals Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacleChelonibia testudinaria(Linnaeus, 1758)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2019 ◽  
Author(s):  
Christine Ewers-Saucedo ◽  
John D. Zardus ◽  
John P. Wares
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Next Generation Sequencing Data ◽  
Model Organisms ◽  
Next Generation ◽  
Sequencing Data ◽  
Genetic Studies ◽  
Evolutionary Features ◽  
Generation Sequencing

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacleChelonibia testudinaria(Linnaeus, 1758).Chelonibia testudinariaappears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies onC. testudinaria.

Efficient application of next-generation sequencing for the diagnosis of rare genetic syndromes

2014 ◽  
Vol 67 (12) ◽  
pp. 1099-1103 ◽  
Author(s):  
Irene Madrigal ◽  
Maria Isabel Alvarez-Mora ◽  
Olof Karlberg ◽  
Laia Rodríguez-Revenga ◽  
Dei M Elurbe ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Next Generation Sequencing ◽  
Genetic Diseases ◽  
Genetic Defect ◽  
Disease Diagnosis ◽  
Underlying Disease ◽  
Next Generation ◽  
Genetic Syndromes ◽  
Biomedical Diagnosis ◽  
Generation Sequencing

AimsThe causes of intellectual disability, which affects 1%–3% of the general population, are highly heterogeneous and the genetic defect remains unknown in around 40% of patients. The application of next-generation sequencing is changing the nature of biomedical diagnosis. This technology has quickly become the method of choice for searching for pathogenic mutations in rare uncharacterised genetic diseases.MethodsWhole-exome sequencing was applied to a series of families affected with intellectual disability in order to identify variants underlying disease phenotypes.ResultsWe present data of three families in which we identified the disease-causing mutations and which benefited from receiving a clinical diagnosis: Cornelia de Lange, Cohen syndrome and Dent-2 disease. The genetic heterogeneity and the variability in clinical presentation of these disorders could explain why these patients are difficult to diagnose.ConclusionsThe accessibility to next-generation sequencing allows clinicians to save much time and cost in identifying the aetiology of rare diseases. The presented cases are excellent examples that demonstrate the efficacy of next-generation sequencing in rare disease diagnosis.

scholarly journals xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments

2018 ◽  
Author(s):  
Jesse Farek ◽  
Daniel Hughes ◽  
Adam Mansfield ◽  
Olga Krasheninina ◽  
Waleed Nasser ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Rapid Development ◽  
Variant Calling ◽  
Supplementary Information ◽  
Data Generation ◽  
Next Generation ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
Homogeneous Sample ◽  
Generation Sequencing

AbstractMotivationThe rapid development of next-generation sequencing (NGS) technologies has lowered the barriers to genomic data generation, resulting in millions of samples sequenced across diverse experimental designs. The growing volume and heterogeneity of these sequencing data complicate the further optimization of methods for identifying DNA variation, especially considering that curated highconfidence variant call sets commonly used to evaluate these methods are generally developed by reference to results from the analysis of comparatively small and homogeneous sample sets.ResultsWe have developed xAtlas, an application for the identification of single nucleotide variants (SNV) and small insertions and deletions (indels) in NGS data. xAtlas is easily scalable and enables execution and retraining with rapid development cycles. Generation of variant calls in VCF or gVCF format from BAM or CRAM alignments is accomplished in less than one CPU-hour per 30× short-read human whole-genome. The retraining capabilities of xAtlas allow its core variant evaluation models to be optimized on new sample data and user-defined truth sets. Obtaining SNV and indels calls from xAtlas can be achieved more than 40 times faster than established methods while retaining the same accuracy.AvailabilityFreely available under a BSD 3-clause license at https://github.com/jfarek/[email protected] informationSupplementary data are available at Bioinformatics online.

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