Patients with PMD who are thoroughly screened by Genomic medicine have a considerable chance of benefiting greatly from whole-genome sequencing

2021 ◽  
Author(s):  
Moataz Dowaidar
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Direct Sequencing ◽  
Genomic Medicine ◽  
Diagnostic Process ◽  
Whole Genome ◽  
Rna Seq ◽  
Tissue Samples ◽  
Long Read ◽  
Major Transition

It appears that the role of genetics in neurology is undergoing a major transition in the present. The scope of genomic medicine has advanced from the only realm of academic investigation to the well-established and widely accepted instrument for genetic labs. Previously, this test was reserved for the most challenging patients, but today it is being utilized as a first step in looking at rare inherited neurological disorders. Researchers and clinicians working in the field of mitochondrial medicine will need to employ new laboratory techniques and DNA sequencing technology in order to move forward with future diagnosis methods and cut down on research time. Patients with PMD who are thoroughly screened have a considerable chance of benefiting greatly from whole-genome sequencing (WGS) at the beginning of their diagnostic process. Using long-read sequencing, there is the potential to help in the discovery of new genetic causes of PMD, the resolution of phasing issues, and the advancement of RNA and mtDNA investigations by way of direct sequencing. With the use of a great number of tissue samples from patients with PMD, there are significant advantages which can greatly promote the quick implementation of this technique into diagnostic laboratories. As RNA-seq technology is introduced into diagnostic laboratories, it will serve as an accurate means to examine the entire spectrum of disease while providing support for difficult cases. The plentiful supply of tissue samples from patients with PMD further enhances the ability of RNA-seq to rapidly be adopted in these laboratories. Finally, more validation of innovative tRNA approaches will be required in order to determine the pathogenicity of this common group of mtDNA-related PMDs.

scholarly journals Continuing the sequence? Towards an economic evaluation of whole genome sequencing for the diagnosis of rare diseases in Scotland

2021 ◽  
Author(s):  
Michael Abbott ◽  
Lynda McKenzie ◽  
Blanca Viridiana Guizar Moran ◽  
Sebastian Heidenreich ◽  
Rodolfo Hernández ◽  
...  
Keyword(s):  
Economic Evaluation ◽  
Genetic Testing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rare Diseases ◽  
Genomic Medicine ◽  
Future Research ◽  
Clinical Genetics ◽  
Whole Genome ◽  
Peace Of Mind

AbstractNovel developments in genomic medicine may reduce the length of the diagnostic odyssey for patients with rare diseases. Health providers must thus decide whether to offer genome sequencing for the diagnosis of rare conditions in a routine clinical setting. We estimated the costs of singleton standard genetic testing and trio-based whole genome sequencing (WGS), in the context of the Scottish Genomes Partnership (SGP) study. We also explored what users value about genomic sequencing. Insights from the costing and value assessments will inform a subsequent economic evaluation of genomic medicine in Scotland. An average cost of £1,841 per singleton was estimated for the standard genetic testing pathway, with significant variability between phenotypes. WGS cost £6625 per family trio, but this estimate reflects the use of WGS during the SGP project and large cost savings may be realised if sequencing was scaled up. Patients and families valued (i) the chance of receiving a diagnosis (and the peace of mind and closure that brings); (ii) the information provided by WGS (including implications for family planning and secondary findings); and (iii) contributions to future research. Our costings will be updated to address limitations of the current study for incorporation in budget impact modelling and cost-effectiveness analysis (cost per diagnostic yield). Our insights into the benefits of WGS will guide the development of a discrete choice experiment valuation study. This will inform a user-perspective cost–benefit analysis of genome-wide sequencing, accounting for the broader non-health outcomes. Taken together, our research will inform the long-term strategic development of NHS Scotland clinical genetics testing services, and will be of benefit to others seeking to undertake similar evaluations in different contexts.

scholarly journals Identifying Aspects of Public Attitudes Toward Whole Genome Sequencing to Inform the Integration of Genomics into Care

2021 ◽  
pp. 1-12
Author(s):  
Holly Etchegary ◽  
Daryl Pullman ◽  
Charlene Simmonds ◽  
Zoha Rabie ◽  
Proton Rahman
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Online Survey ◽  
Public Attitudes ◽  
Genetic Counselor ◽  
Genomic Medicine ◽  
Genomic Data ◽  
Whole Genome ◽  
The Public ◽  
Genomic Test

<b><i>Introduction:</i></b> The growth of global sequencing initiatives and commercial genomic test offerings suggests the public will increasingly be confronted with decisions about sequencing. Understanding public attitudes can assist efforts to integrate sequencing into care and inform the development of public education and outreach strategies. <b><i>Methods:</i></b> A 48-item online survey was advertised on Facebook in Eastern Canada and hosted on SurveyMonkey in late 2018. The survey measured public interest in whole genome sequencing and attitudes toward various aspects of sequencing using vignettes, scaled, and open-ended items. <b><i>Results:</i></b> While interest in sequencing was high, critical attitudes were observed. In particular, items measuring features of patient control and choice regarding genomic data were strongly endorsed by respondents. Majority wanted to specify upfront how their data could be used, retain the ability to withdraw their sample at a later date, sign a written consent form, and speak to a genetic counselor prior to sequencing. Concerns about privacy and unauthorized access to data were frequently observed. Education level was the sociodemographic variable most often related to attitude statements such that those with higher levels of education generally displayed more critical attitudes. <b><i>Conclusions:</i></b> Attitudes identified here could be used to inform the development of implementation strategies for genomic medicine. Findings suggest health systems must address patient concerns about privacy, consent practices, and the strong desire to control what happens to their genomic data through public outreach and education. Specific oversight procedures and policies that are clearly communicated to the public will be required.

Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

2018 ◽  
Vol 64 (3) ◽  
pp. 191-197 ◽  
Author(s):  
Takeshi Mizuguchi ◽  
Tomoko Toyota ◽  
Hiroaki Adachi ◽  
Noriko Miyake ◽  
Naomichi Matsumoto ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Repeat Expansion ◽  
Whole Genome ◽  
Smrt Sequencing ◽  
Long Read

scholarly journals Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome

2021 ◽  
Author(s):  
Yu-Sheng Chen ◽  
Shuaiyao Lu ◽  
Bing Zhang ◽  
Tingfu Du ◽  
Wen-Jie Li ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Comprehensive Analysis ◽  
Host Genome ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Rna Seq ◽  
Sequencing Data ◽  
Infected Cells

SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didn't identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2's integration into host genome is lacking.

scholarly journals Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

2018 ◽  
Vol 12 (6) ◽  
pp. e0006566 ◽  
Author(s):  
Elizabeth M. Batty ◽  
Suwittra Chaemchuen ◽  
Stuart Blacksell ◽  
Allen L. Richards ◽  
Daniel Paris ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Orientia Tsutsugamushi ◽  
Human Pathogen ◽  
Long Read

scholarly journals 6 Translating genomics for clinical benefit

2019 ◽  
Vol 95 (1130) ◽  
pp. 686.3-686
Author(s):  
Mark Caulfield
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Medicine ◽  
Health Gain ◽  
Annual Review ◽  
Whole Genome ◽  
Department Of Health ◽  
Data Points ◽  
Genome Analyses ◽  
The Uk

The UK 100,000 Genomes Project has focussed on transforming genomic medicine in the National Health Service using whole genome sequencing in rare disease, cancer and infection. Genomics England partnering with the NHS established 13 Genomic Medicine Centres, the NHS whole genome sequencing centre and the Genomics England Clinical Interpretation Partnership (3337 researchers from 24 countries). We sequenced the 100,000th genome on the 5th December 2019 and completed an initial analysis for participants in July 2019. Alongside these genomes we have assembled a longitudinal life course dataset for research and diagnosis including 2.6 billion clinical data points for the 3000 plus researchers to work on to drive up the value of the genomes for direct healthcare. In parallel we have partnered the NHS to establish one of the world’s most advanced Genomic Medicine Service where we re-evaluated 300,000 genomic tests and upgraded 25% of tests to newer technologies with an annual review. The Department of Health have announced the ambition to undertake 5 million genome analyses over the next 5 years focused on new areas tractable to health gain.

Abstract 4281: Targeted or whole genome sequencing of formalin-fixed tissue samples

2014 ◽  
Author(s):  
Sarah Munchel ◽  
Yen Hoang ◽  
Yue Zhao ◽  
Joseph Cottrell ◽  
Brandy Klotzle ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Fixed Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Tissue ◽  
Formalin Fixed

scholarly journals Multidrug-Resistant Proteus mirabilis Strain with Cointegrate Plasmid

2020 ◽  
Vol 8 (11) ◽  
pp. 1775
Author(s):  
Andrey Shelenkov ◽  
Lyudmila Petrova ◽  
Valeria Fomina ◽  
Mikhail Zamyatin ◽  
Yulia Mikhaylova ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Proteus Mirabilis ◽  
Intestinal Microflora ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Long Read ◽  
Tract Infections ◽  
Eskape Pathogens

Proteus mirabilis is a component of the normal intestinal microflora of humans and animals, but can cause urinary tract infections and even sepsis in hospital settings. In recent years, the number of multidrug-resistant P. mirabilis isolates, including the ones producing extended-spectrum β-lactamases (ESBLs), is increasing worldwide. However, the number of investigations dedicated to this species, especially, whole-genome sequencing, is much lower in comparison to the members of the ESKAPE pathogens group. This study presents a detailed analysis of clinical multidrug-resistant ESBL-producing P. mirabilis isolate using short- and long-read whole-genome sequencing, which allowed us to reveal possible horizontal gene transfer between Klebsiella pneumoniae and P. mirabilis plasmids and to locate the CRISPR-Cas system in the genome together with its probable phage targets, as well as multiple virulence genes. We believe that the data presented will contribute to the understanding of antibiotic resistance acquisition and virulence mechanisms for this important pathogen.

Sign in / Sign up

Export Citation Format

Share Document