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Next Generation Sequencing - Articles and news items

data-driven-technology

Democratising the Data-Driven Medicine revolution

Blog, Z Homepage promo / 7 November 2016 / Jurgi Camblong, CEO and co-founder of Sophia Genetics

Sophia Genetics’ CEO Jurgi Camblong says genomic data can now diagnose and tailor individual treatments but how do we democratise Data-Driven Medicine?

NEB® launches new NEBNext® Ultra™ II Kit for NGS Library Preparation with as little as 500 pg of input DNA

NEB® launches new NEBNext® Ultra™ II Kit for NGS Library Preparation with as little as 500 pg of input DNA

Supplier news / 4 November 2015 / New England BioLabs, Inc.

New Ultra II technology addresses lower input amounts and challenging sample types for Illumina® next generation sequencing systems…

Next-generation transcriptomic analysis in cancer vascular research

Next-generation transcriptomic analysis in cancer vascular research

Genomics, Issue 4 2015 / 3 September 2015 / Joseph W. Wragg and Roy Bicknell, University of Birmingham

Over the past decade significant advances have been made in the fields of genomic and transcriptomic profiling, inspired by the advent of next-generation sequencing (NGS). Yet despite the considerable promise of these new technologies, uptake has been slow. The focus of this review is the use of next-generation transcriptomic analysis in the field of cancer endothelial biology, highlighting its advantages and a few of the disadvantages compared with current-generation technologies…

René Dirks, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS)

Understanding early mouse embryonic development using single-cell mRNA Sequencing

Genomics, Issue 3 2014 / 3 July 2014 / René Dirks and Hendrik Marks, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS)

Biomedical research often involves the use of cell lines that can be cultured in a laboratory. Individual cells within such cell lines often share a similar morphology. A remarkable exception are in vitro cultured mouse Embryonic Stem Cells (mESCs) – pluripotent cells derived from the blastocyst stage of the mouse developing embryo. Different from many other cell lines, mESCs show heterogeneity in morphology and gene expression between the individual cells within a population. This heterogeneity makes it challenging to characterise mESCs at a molecular level, since global profiling methods generally require large numbers of cells. However, new methods and technologies allow global transcriptome profiling of individual cells. By capturing the global transcriptome of many individual cells using single-cell next-generation mRNA-sequencing, our research focuses on the identification of novel transcription factor modules that contribute to the unique pluripotent state of mESCs, as well as to the differentiation of mESCs, as a model for early mouse embryonic development…

Roche acquires in vitro diagnostics company GeneWEAVE

Next generation sequencing: Application of next generation sequencing to preclinical cancer model profiling

Genomics, Issue 6 2013 / 15 December 2013 / James R. Bradford, Oncology iMED, AstraZeneca Pharmaceuticals

Preclinical cancer models allow us to gain insight into therapeutic potential and mechanism of anti-cancer agents early in the drug discovery process. Whilst traditional array-based approaches have made a significant contribution to the characterisation of these models, the advent of next generation sequencing has revolutionised genomic research and is anticipated to make a huge impact on our understanding of preclinical models, leading to more targeted therapies for cancer patients. This article provides an overview of next generation sequencing in the context of cancer model profiling and evaluates the choice of technologies available and their application to both in vitro and in vivo model characterisation…

Next Generation Sequencing

Next generation sequencing: Using RNAseq to identify anti-cancer targets in the tumour vasculature

Genomics, Issue 6 2013 / 15 December 2013 / Klarke M. Sample and Roy Bicknell, University of Birmingham

It is possible to attack the vasculature within solid tumours and achieve an anti-cancer effect. In the last decade, a number of studies have utilised cDNA libraries, SAGE analysis and microarrays to identify potential drug targets in the tumour endothelium. Modern sequencing technologies are likely to be a far more powerful and comprehensive tool for characterising the endothelial transcriptome…

Cancer Research UK drug launched in its first clinical trial

Future trends in drug discovery technology

Drug Discovery, Issue 6 2012 / 18 December 2012 / Terry McCann, TJM Consultancy

The average cost to a major pharmaceutical company of developing a new drug is over USD 6 billion. Herper observes that the pharmaceutical industry is gripped by rising failure rates and costs, and suggests that the cost of new drugs will be reduced by new technologies and deeper understanding of biology. While the objectives of drug discovery don’t change, the methods and techniques by which pharmaceutical companies, biotechs and academia discover new drugs are evolving at a significant pace – and they need to. Drug discovery scientists are all aiming to identify compounds and candidate drugs with ‘good’ properties that are safe and efficacious, as quickly and cheaply as possible. The standard approach of the last 20 years has been to identify a single molecule disease target, and then to identify a compound that interacts with and modulates this target with high specificity. However, there is now a growing realisation that this ‘one target – one drug’ approach doesn’t work well, and that screening huge libraries of compounds against one particular property of an isolated target is an inefficient way to discover potential drugs. Much of the innovation currently seen in drug discovery methodologies seeks to access and integrate more information – about targets, compounds, and disease phenotypes – to enable a more comprehensive and holistic approach to discovering ‘good’ drug candidates. This article does not try to crystal ball-gaze deep into the future, but rather to identify those trends in the adoption of new technologies and approaches that are gaining traction now, and that can be expected to become more prevalent in the next two to three years…

FIGURE 1 The rapid evolution of sequencing technologies. A. First generation Sanger sequencing technology. B. Second ‘Next’ generation massively parallel sequencing technology (454 Sequencing © Roche Diagnostics) C. Third ‘Next-Next’ generation single molecule, real-time sequencing technology. In the coming years, second or third generation technologies may develop to an extent where a human genome can be sequenced for a USD 1,000 in a matter of hours

DNA sequencing technologies and emerging applications in drug discovery

Genomics, Issue 6 2011 / 13 December 2011 / Nalini A.L. Mehta & David J. Dow, Molecular and Cellular Technologies, Platform Technology and Science, GlaxoSmithKline and Anthony M. Battram, Molecular and Cellular Technologies, Platform Technology and Science, GlaxoSmithKline & Department of Life Sciences, Imperial College London

In recent years, the development of Next Generation DNA Sequencing (NGS) technology has significantly impacted molecular biology research, resulting in many new insights and discoveries. NGS technology goes beyond traditional DNA sequencing with applications that reach across the central dogma of molecular biology from DNA to RNA and protein science. Drug discovery is beginning to benefit from the diversity of NGS, with applications in evidence across various therapeutic areas, such as oncology, immunology and infectious diseases.

DNA is the molecule of life, containing the information for the synthesis of RNA molecules and proteins, which in turn form structural components of the cell or catalyse essential biochemical processes. Understanding the sequence of DNA, which is made from the four basic building blocks or ‘nucleotides’, A,G,C and T, has resulted in great insights and discoveries in cellular biology, pathology and disease, culminating in the human genome project, which achieved the remarkable feat of determining the sequence of the three billion bases of the human genome.

The field of DNA sequencing has witnessed some key milestones in technology develop – ment since the description of the first revolutionary DNA sequencing techniques in 19771,2. The Sanger dideoxy sequencing method, discovered by the Nobel Laureate Fred Sanger, underwent the most significant improvements and became the first automated sequencing platform in the late 20th century. Advancements in the Sanger process were partly motivated by the advent of the USD 3 billion Human Genome Project, which required the development of high-throughput tech – niques3,4 (Figure 1A).

Genomics Sequencing supplement

Genomics / Sequencing supplement 2011

Genomics, Issue 4 2011, Supplements / 31 August 2011 / Bhupinder Bhullar (Novartis Pharma AG), Wei Chen (Max Delbrück Center for Mollecular Medicine Berlin-Buch), Stephen A. Haney (Biological Profiling, Applied Quantitative Genotherapeutics, Pfizer Biotechnologies Unit)

NGS powers up drug discovery and healthcare.
Impact of novel sequencing technology on transcriptome analysis.
Making sense of nonesense (and missense): Bringing the results of recent genetic studies into the drug discovery laboratory.

DNA sequencing

Next Generation Sequencing: Current realities in cancer biology

Cancer Biology, Issue 1 2011 / 16 February 2011 / Ross Sibson, Director of Research, Applied Cancer Biology Group, University of Liverpool

The rate of progress in molecular cell biological sciences has become dramatic. This is fuelled in part by developments in technology, none more so than in the field of nucleic acid sequencing. So-called Next Generation Sequencing Platforms promise to revolutionise our understanding of the importance of genetic differences on an individual basis. According to the modern personalised or stratified medicine paradigms, this will revolutionise current practices in terms of early detection, treatment, diagnosis, prognosis and even prevention. Revolutions are apt to disappoint and drug pipelines have yet to justify such optimism yet molecular geneticists can point already to notable successes like the completion of their flagship project, the human genome in 2001, within time and within budget. What are the current realities? The field of cancer serves as an excellent test and would suggest that advances are being made incrementally but rapidly.

PCR Viability

PCR and personalised cancer medicine

Genomics, Issue 6 2010 / 16 December 2010 / Frank McCaughan, MRC Career Development Fellow, MRC Laboratory of Molecular Biology

The delivery of personalised medicine is a key goal of modern cancer medicine and refers to the tailoring of anticancer therapy to the molecular characteristics of an individual tumour. To facilitate personalised medicine, it is important to have robust and reproducible means of gaining molecular information about a patient’s cancer that can be used to guide clinical decision-making. There have therefore been tremendous efforts to identify molecular signatures – biomarkers – that can be used to help predict a cancer patient’s prognosis or their likelihood of a response to targeted drug therapies. Such molecular profiling has long been applied to haematological malignancies and is increasingly becoming the norm in the most common epithelial cancers such as lung and colorectal cancer. This article will focus on the role of the polymerase chain reaction (PCR) in helping to meet the challenges involved in the design, testing and delivery of personalised cancer medicine.

Figure 1 Advances in the development of sequencing technologies have resulted in an increase in data output with a dramatic decrease in cost. This graph compares calculated sequencing costs for one complete haploid human genome sequence (23 chromosomes, three billion bases) * estimated from literature ** marketing figures

The Sequencing Revolution: enabling personal genomics and personalised medicine

Genomics, Issue 5 2010 / 29 October 2010 / Bhupinder Bhullar, Novartis Institute for Biomedical Research

It has been 10 years since the completion of the first draft of the human genome. Today, we are in the midst of a full assault on the human genetic code, racing to uncover the genetic mechanisms that affect disease, aging, happiness, violence … and just about every imaginable human variation. Advances in DNA sequencing technology have enabled individuals to have their own genomes sequenced rapidly, cheaply and in astonishing detail. The sequencing revolution is also changing the way the pharmaceutical industry develops, tests and targets new medicines.

 

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