scholarly journals Improving diagnostics of rare genetic diseases with NGS approaches

2021 ◽  
Author(s):  
Mateja Vinkšel ◽  
Karin Writzl ◽  
Aleš Maver ◽  
Borut Peterlin
Keyword(s):  
Health Systems ◽  
Rare Diseases ◽  
Genetic Diseases ◽  
Cross Border ◽  
Novel Technology ◽  
Rare Genetic Diseases ◽  
Diagnostic Hypothesis ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing

AbstractAccording to a rough estimate, one in fifteen people worldwide is affected by a rare disease. Rare diseases are therefore common in clinical practice; however, timely diagnosis of rare diseases is still challenging. Introduction of novel methods based on next-generation sequencing (NGS) technology offers a successful diagnosis of genetically heterogeneous disorders, even in case of unclear clinical diagnostic hypothesis. However, the application of novel technology differs among the centres and health systems significantly. Our goal is to discuss the impact of the implementation of NGS in the diagnosis of rare diseases and present advantages along with challenges of diagnostic approach. Systematic implementation of NGS in health systems can significantly improve the access of patients with rare diseases to diagnosis and reduce the dependence of national health systems for cross-border collaboration.

scholarly journals The long tail and rare disease research: the impact of next-generation sequencing for rare Mendelian disorders

2015 ◽  
Vol 97 ◽  
Author(s):  
TONY SHEN ◽  
ARIEL LEE ◽  
CAROL SHEN ◽  
C.JIMMY LIN
Keyword(s):  
Next Generation Sequencing ◽  
Rare Diseases ◽  
The United States ◽  
Next Generation ◽  
Recent Developments ◽  
Low Incidence ◽  
The Cost ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing

SummaryThere are an estimated 6000–8000 rare Mendelian diseases that collectively affect 30 million individuals in the United States. The low incidence and prevalence of these diseases present significant challenges to improving diagnostics and treatments. Next-generation sequencing (NGS) technologies have revolutionized research of rare diseases. This article will first comment on the effectiveness of NGS through the lens of long-tailed economics. We then provide an overview of recent developments and challenges of NGS-based research on rare diseases. As the quality of NGS studies improve and the cost of sequencing decreases, NGS will continue to make a significant impact on the study of rare diseases moving forward.

Ethics and equity in rare disease research and healthcare

2021 ◽  
Author(s):  
Maria Koromina ◽  
Vasileios Fanaras ◽  
Gareth Baynam ◽  
Christina Mitropoulou ◽  
George P Patrinos
Keyword(s):  
Rare Diseases ◽  
Ethical Issues ◽  
Genetic Diseases ◽  
Ethical Framework ◽  
Middle Income ◽  
Next Generation Sequencing Technology ◽  
Ethical Frameworks ◽  
Rare Genetic Diseases ◽  
Conducting Research ◽  
Key Aspects

Rapid advances in next-generation sequencing technology, particularly whole exome sequencing and whole genome sequencing, have greatly affected our understanding of genetic variation underlying rare genetic diseases. Herein, we describe ethical principles of guiding consent and sharing of genomics research data. We also discuss ethical dilemmas in rare diseases research and patient recruitment policies and address bioethical and societal aspects influencing the ethical framework for genetic testing. Moreover, we focus on addressing ethical issues surrounding research in low- and middle-income countries. Overall, this perspective aims to address key aspects and issues for building proper ethical frameworks, when conducting research involving genomics data with a particular emphasis on rare diseases and genetics testing.

Machine Learning Perspective in Cancer Research

2021 ◽  
pp. 142-163
Author(s):  
Aman Sharma ◽  
Rinkle Rani
Keyword(s):  
Machine Learning ◽  
Cancer Research ◽  
Expression Profiles ◽  
Genetic Diseases ◽  
Cost Effective ◽  
Healthcare Sector ◽  
Diagnosis And Prognosis ◽  
Cost Effective Approach ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Advancement in genome sequencing technology has empowered researchers to think beyond their imagination. Researchers are trying their hard to fight against various genetic diseases like cancer. Artificial intelligence has empowered research in the healthcare sector. Moreover, the availability of opensource healthcare datasets has motivated the researchers to develop applications which can help in early diagnosis and prognosis of diseases. Further, next-generation sequencing (NGS) has helped to look into detailed intricacies of biological systems. It has provided an efficient and cost-effective approach with higher accuracy. The advent of microRNAs also known as small noncoding genes has begun the paradigm shift in oncological research. We are now able to profile expression profiles of RNAs using RNA-seq data. microRNA profiling has helped in uncovering their relationship in various genetic and biological processes. Here in this chapter, the authors present a review of the machine learning perspective in cancer research.

scholarly journals Reference exome data for a Northern Brazilian population

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Alexia L. Weeks ◽  
Richard W. Francis ◽  
Joao I. C. F. Neri ◽  
Nathaly M. C. Costa ◽  
Nivea M. R. Arrais ◽  
...  
Keyword(s):  
Rare Diseases ◽  
Sequence Data ◽  
Genetic Diseases ◽  
Specific Reference ◽  
Single Nucleotide Variants ◽  
Data Set ◽  
Single Nucleotide ◽  
Rare Genetic Diseases ◽  
Genetics And Genomics ◽  
Brazilian Cohort

Abstract Exome sequencing is widely used in the diagnosis of rare genetic diseases and provides useful variant data for analysis of complex diseases. There is not always adequate population-specific reference data to assist in assigning a diagnostic variant to a specific clinical condition. Here we provide a catalogue of variants called after sequencing the exomes of 45 babies from Rio Grande do Nord in Brazil. Sequence data were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. A total of 612,761 variants were identified in at least one individual in this Brazilian Cohort, including 559,448 single nucleotide variants (SNVs) and 53,313 insertion/deletions. Of these, 58,111 overlapped with nonsynonymous (nsSNVs) or splice site (ssSNVs) SNVs in dbNSFP. As an aid to clinical diagnosis of rare diseases, we used the American College of Medicine Genetics and Genomics (ACMG) guidelines to assign pathogenic/likely pathogenic status to 185 (0.32%) of the 58,111 nsSNVs and ssSNVs. Our data set provides a useful reference point for diagnosis of rare diseases in Brazil. (169 words).

scholarly journals SARS-CoV-2 as a Trigger in the Development of Tourette’s-Like Symptoms: A Case Report

2021 ◽  
Author(s):  
Sabine Hazan ◽  
Sheldon Jordan
Keyword(s):  
Case Report ◽  
Next Generation Sequencing ◽  
Gut Microbiota ◽  
Dramatic Improvement ◽  
Next Generation ◽  
Rt Pcr ◽  
Gastrointestinal Microbiota ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing

Abstract Background: Reports have been surfacing surrounding CNS-associated symptoms in individuals affected by coronavirus disease 19 (COVID-19). Tourette syndrome is a neuropsychiatric disorder with usual onset in childhood. Gut microbiota can affect central physiology and function via the microbiota-gut-brain axis. The authors of this case report describe Tourette’s-like symptoms in a patient resulting from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection disrupting gut microbiota. Case Presentation: This case involves a 16-year-old female that developed acute onset Tourette’s-like symptoms along with neuropsychiatric symptoms after exposure to and infection from SARS-CoV-2. The patient had negative nasopharyngeal (NP) real-time reverse transcription-PCR (RT-PCR) tests for SARS-CoV-2 on five occasions from August of 2020 through June of 2021. The patient’s symptoms continued to worsen over the next six months until next-generation sequencing (NGS) revealed SARS-CoV-2 in her stool. Her treatment was adjusted as NGS revealed SARS-CoV-2 in her stool. Repair of the gastrointestinal microbiota, treatment with nutraceutical and pharmaceutical agents, as well as alterations in her surroundings resulted in dramatic improvement in the microbiome and a significant reduction of symptoms.Discussion: The use of (RT-PCR) testing to determine the presence or absence of SARS-CoV-2 may be inadequate and inaccurate for individuals that have been exposed to the virus. In addition, the impact of SARS-CoV-2 infection of the GI tract may cause significant havoc in the gut microbiota. Additional testing, eradication of infectious agents, as well as restoration of the gut microbiome are needed to effectively manage and treat this condition. The patient’s symptoms worsened over the next six months until next-generation sequencing (NGS) revealed SARS-CoV-2 in her stool and her treatment was adjusted. Treatment with nutraceuticals and alterations in her surroundings was followed by a more normal microbiome and a dramatic reduction in symptoms.

scholarly journals Rett syndrome in Russia and abroad: a scientific historical review

2020 ◽  
Vol 65 (3) ◽  
pp. 25-31
Author(s):  
S. G. Vorsanova ◽  
Yu. B. Yurov ◽  
V. Yu. Voinova ◽  
I. Yu. Yurov
Keyword(s):  
Rett Syndrome ◽  
Rare Diseases ◽  
Gene Sequence ◽  
Genetic Diseases ◽  
Historical Review ◽  
Mecp2 Gene ◽  
Cellular Mechanisms ◽  
Rare Genetic Diseases ◽  
Present Information ◽  
Genomic Disorders

This review presents the theoretical, practical and geographical aspects of Rett syndrome and other rare diseases, according to the data of the last VIII International Congress in Russia, and the main publications on Rett syndrome. The issues highlighted by the participants remain relevant and determine the direction of modern studies. The presentations made at the symposium helped to form a global concept of the molecular and cellular mechanisms of Rett syndrome and a number of rare genetic/genomic diseases. The article presents a number of domestic findings in the field of Rett syndrome and other rare diseases. The authors also present information on rare diseases associated with the Rett-like-phenotype or with mutations/variations of the MECP2 gene sequence copies. The authors consider the identified chromosomal (genomic) disorders / diseases in the context of rare diseases. This approach to the Rett syndrome studies analysis is quite new in the world research practice. We hope this review to become valuable not only for specialists in the field of rare genetic diseases, but also for the scientists and clinicians studying Rett syndrome and for physicians (pediatricians, geneticists, neurologists, psychiatrists) meeting these patients in their practice.

scholarly journals RDmap: A Map for Exploring Rare Diseases

2021 ◽  
Author(s):  
Jian Yang ◽  
Cong Dong ◽  
Huilong Duan ◽  
Qiang Shu ◽  
Haomin Li
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Genetic Diseases ◽  
Distance Matrix ◽  
Disease Diagnosis ◽  
Human Phenotype ◽  
Pathogenic Genes ◽  
Disease Information ◽  
Rare Genetic Diseases ◽  
Interactive Map

Abstract Background: The complexity of the phenotypic characteristics and molecular bases of many rare human genetic diseases makes the diagnosis of such diseases a challenge for clinicians. A map for visualizing, locating and navigating rare diseases based on similarity will help clinicians and researchers understand and easily explore these diseases. Methods: A distance matrix of rare diseases included in Orphanet was measured by calculating the quantitative distance among phenotypes and pathogenic genes based on Human Phenotype Ontology (HPO) and Gene Ontology (GO), and each disease was mapped into Euclidean space. A rare disease map, enhanced by clustering classes and disease information, was developed based on ECharts. Results: A rare disease map called RDmap was published at http://rdmap.nbscn.org. Total 3,287 rare diseases are included in the phenotype-based map, and 3,789 rare genetic diseases are included in the gene-based map; 1,718 overlapping diseases are connected between two maps. RDmap works similarly to the widely used Google Map service and supports zooming and panning. The phenotype similarity base disease location function performed better than traditional keyword searches in an in silico evaluation, and 20 published cases of rare diseases also demonstrated that RDmap can assist clinicians in seeking the rare disease diagnosis. Conclusion: RDmap is the first user-interactive map-style rare disease knowledgebase. It will help clinicians and researchers explore the increasingly complicated realm of rare genetic diseases.

scholarly journals Next Generation Sequencing (NGS) and patient pathways: What is the impact on clinical decision?

2018 ◽  
Vol 29 ◽  
pp. vi14-vi15
Author(s):  
S. Coquerelle ◽  
M. Darlington ◽  
M. Michel ◽  
M. Durand ◽  
J. Gutton ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Decision ◽  
Next Generation ◽  
Patient Pathways ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing

scholarly journals The Impact of Next Generation Sequencing in Cancer Research

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2928
Author(s):  
Katia Nones ◽  
Ann-Marie Patch
Keyword(s):  
Cancer Research ◽  
Next Generation Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Next Generation ◽  
Parallel Sequencing ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing ◽  
Technical Revolution

Next generation sequencing (NGS) describes the technical revolution that enabled massively parallel sequencing of fragmented nucleic acids, thus making possible our current genomic understanding of cancers [...]

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