Next Generation Sequencing
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New generation sequencing method - Illumina platform

This chanel develops and host various educational videos in the field of agriculture and applied genomics which will help for the students, teachers, scienti...
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A Guide to Targeted NGS: Generating Accurate Data for Personalized Medicine

A Guide to Targeted NGS: Generating Accurate Data for Personalized Medicine | Next Generation Sequencing | Scoop.it
As personalized medicine is integrated into mainstream medical treatment, sequencing clinically relevant genes using the latest next generation sequencing (NGS) technologies will prove instrumental in guiding clinicians towards informed treatment decisions.
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Next-Generation Sequencing Offers Insight Into How Species Adapt To Climate Change

 onNGS offers insight into how species adapt to climate change. NGS has made it possible to analyze enormous numbers of short pieces of DNA very quickly, and this technology is already revolutionizing the biomedical sciences.

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Not only in biomedical sciences, but NGS is now very useful also in ecological studies by iluminating into the way populations are adapting to an environment changing. 

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FDA Considering How to Tailor its Oversight for Next Generation Sequencing | FDA Voice

FDA Considering How to Tailor its Oversight for Next Generation Sequencing | FDA Voice | Next Generation Sequencing | Scoop.it
#FDAVoice: FDA Considering How to Tailor its Oversight for Next Generation Sequencing http://t.co/C7H6Qaapvx
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FDA has been reviewing the current regulatory landscape involving next generation sequencing as the technology moves rapidly from research to clinical practice 

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GEN | Magazine Articles:NGS Ready for Clinical Oncology Testing

GEN | Magazine Articles:NGS Ready for Clinical Oncology Testing | Next Generation Sequencing | Scoop.it
One, two, or even a few genomic “hotspots” just aren’t enough for clinical genomics to catch fire, but it soon may be set ablaze by whole-exome and whole-genome sequencing.
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SeqCap EZ Workflow with the KAPA Library Preparation Kits

SeqCap EZ Workflow with the KAPA Library Preparation Kits.
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NATURE: The Method of the Year for 2013 is… single-cell sequencing

NATURE: The Method of the Year for 2013 is… single-cell sequencing | Next Generation Sequencing | Scoop.it

Single-cell sequencing edged out other contenders as our choice of Method of the Year in 2013. These techniques really came into their own in 2013 and are fast providing new insights into the workings of single cells that ensemble methods are incapable of.


Back in 2008 we chose next-generation sequencing as our Method of the Year not only because of how the new techniques would improve performance in conventional sequencing applications, but also because they opened up whole new applications, unthinkable with traditional Sanger sequencing. Our choice of Method of the Year in 2013 bears this out, as none of these single-cell sequencing applications would be possible without next-generation sequencing. And in some applications the sequencing is used almost exclusively for identifying and counting tagged molecules.

 

Our choice likely comes as a surprise to all those who were certain that we would pick CRISPR/Cas9 technology for targeted genome modification. This is certainly an exciting technology, and not only for genome engineering, but also for epigenome editing as described in a Method to Watch. But genome editing with engineered nucleases was our pick for the 2011 Method of the Year and although CRISPR/Cas9 provides a huge practical improvement by largely dispensing with the need to engineer the nuclease and relying instead on a programmable guide RNA, the advance over 2011 is mostly one of ease-of-use.

 

Methods to investigate biology at the level of single cells have been of keen interest to Nature Methods since the journal started. Our first research article from Robert Singer described a paraffin-embedded tissue FISH (peT-FISH) method to simultaneously detect expression of several genes in situ in single cells while maintaining tissue morphology (Capodieci, P. 2005). This was followed by many other imaging-based methods for such things as measuring cell growth (Groisman, A. 2006), quantifying mRNA (Raj, A. 2008) and protein (Gordon, A. 2006) levels, profiling intracellular signaling (Krutzik, P.O. & Nolan, G.P. 2006) (Loo, L.-H. 2007) and DNA insertion-site analysis (Schmidt, M. 2008) in single cells.

 

The publication of M. Azim Surani’s article on mRNA-Seq whole-transcriptome analysis of a single cell (Tang, F. 2009) in 2009 helped signal the rise of sequencing-based methods for single-cell analysis. But even two years later the Reviews and Perspectives in our supplement on single-cell analysis were more focused on imaging-based than sequencing-based aproaches to single-cell analysis.

 

It was only in 2013 that we finally saw an explosion of original research articles using or reporting single-cell sequencing methods in Nature-family journals. Numerous studies reported new biological results that relied on sequencing of whole or partial genomes or transcriptomes from single cells.


Nature's Method of the Year special feature has three Commentaries by researchers in the field, including some of the earliest developers and users of methods for single-cell analysis. An Editorial, News Feature and Primer describe our choice and provide helpful background information. We hope you enjoy the selection of articles in our special feature.


Via Dr. Stefan Gruenwald
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Translating Next-Gen Sequencing from the Lab to the Clinic: Challenges and Solutions

The confluence of next-generation sequencing technologies, computational analysis of the data, and the use of targeted therapy in cancer care raises a "perfe...
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The opportunities for Next Generation Sequencing (NSG) as a diagnostic tool are immense

The opportunities for Next Generation Sequencing (NSG) as a diagnostic tool are immense | Next Generation Sequencing | Scoop.it
SOURCE (ED NOTE: To see what NGS is, go to this PDF; essentially, it is a tremendous technological advance that facilitates Gene Mapping) Next-Generation Sequencing from Research to the Clinic In this GEN Market & Tech Analysis report we examine...

   


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Thomas Faltin's curator insight, December 30, 2013 7:55 PM

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Clinical Applications of Next Generation Sequencing

Clinical Applications of Next Generation Sequencing (Clinical Applications of Next Generation Sequencing http://t.co/GeqsHKqtTA via @SlideShare)
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Genotyping by Genome Reducing and Sequencing for Outbred Animals

Genotyping by Genome Reducing and Sequencing for Outbred Animals | Next Generation Sequencing | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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GEN | Magazine Articles: Utility of an Automated Next-Generation Sequencing Panel for Understanding Inherited Disorders

GEN | Magazine Articles: Utility of an Automated Next-Generation Sequencing Panel for Understanding Inherited Disorders | Next Generation Sequencing | Scoop.it
Get the latest in biotechnology through daily news coverage as well as analysis, features, tutorials, webinars, podcasts, and blogs. Learn about the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and commercialization.
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10 Things Exome Sequencing Can’t Do–but Why It’s Still Powerful | Guest Blog, Scientific American Blog Network

10 Things Exome Sequencing Can’t Do–but Why It’s Still Powerful | Guest Blog, Scientific American Blog Network | Next Generation Sequencing | Scoop.it
Sequencing of the exome – the protein-encoding parts of all the genes – is beginning to dominate the genetics journals as well as headlines, thanks to ...
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Dernières innovations en Génomique

Dernières innovations en Génomique | Next Generation Sequencing | Scoop.it

Roche Diagnostics France et PrimaDiag s’associent pour proposer une
solution d’automatisation de la capture de séquences en s'appuyant sur la gamme NimbleGen de Roche associée à la plateforme ACSIA NGS-Capture-Edition de PrimaDiag.

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Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples | Next Generation Sequencing | Scoop.it
by Androniki Psifidi, Chrysostomos I. Dovas, Georgios Bramis, Thomai Lazou, Claire L.
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"'How to choose the DNA extraction method in order to obtain a good quality of DNA bank for NGS"

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GEN | Insight & Intelligence™: New Challenges of Next-Gen Sequencing

GEN | Insight & Intelligence™: New Challenges of Next-Gen Sequencing | Next Generation Sequencing | Scoop.it
Like the hydra of myth, as soon as the head of one NGS problem is cut off, new ones grow in its place.
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Which DNA Library Prep Kit for Ion Torrent Should I Choose

Having trouble deciding which NEBNext Fast DNA Library Prep Set for Ion Torrent to choose? Let Christine explain which set is right for your DNA.
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Next-Generation Sequencing Revolutionizes Discovery of Novel Targeted Therapies in Breast Cancer

Next-Generation Sequencing Revolutionizes Discovery of Novel Targeted Therapies in Breast Cancer | Next Generation Sequencing | Scoop.it

"The most promising novel therapeutics in development for patients with breast cancer focus primarily on targeting activating mutations in combinations that are based on findings from next-generation sequencing, according to Debu Tripathy, MD, in a presentation at MBCC on Friday. “Next-generation sequencing, which was introduced not quite 10 years ago, has really revolutionized our ability to look at the tumor genome in high frequency,” said Tripathy, a professor of Medicine and co-leader of the Women’s Cancers Program at Norris Comprehensive Cancer Center at the University of Southern California. “What we’re finding is that every tumor actually has different genetic abnormalities.” Activating mutations in PI3K, HER2, and JAK2 represent the most promising targets for new drug development. In fact, Tripathy noted that several clinical trials are currently examining treatment combinations in this space. Additionally, other strategies of interest are targeting cyclin-dependent kinase (CDK) inhibitors and histone deacetylase (HDAC) inhibition. In one such study, the CDK 4 and 6 inhibitor palbociclib was explored in combination with letrozole for patients with postmenopausal ER-positive, HER2-negative advanced breast cancer. In an analysis of the phase II study, the combination achieved a statistically significant median progression-free survival (PFS) of 26.1 months compared with 7.5 months for letrozole alone. Based on these findings, the FDA granted palbociclib a Breakthrough Therapy designation for the treatment of patients with breast cancer in April 2013."


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Susan Zager's curator insight, March 8, 2014 2:25 PM
Debu Tripathy, MD, in a presentation at MBCC on Friday discussed the new targeted therapies for breast cancer. The most promising targets for new drug development are activating mutations in PI3K, HER2, and JAK2. Other targets of interest include cyclin-dependent kinase (CDK) inhibitors and histone deacetylase (HDAC) inhibition. While 10% of triple negative breast cancers have androgen receptors,  “triple-negative breast cancer is an area of unmet need. We don’t have other biological therapies approved right now, other than chemotherapy, and it is a more aggressive cancer and more likely to recur,” said Tripathy. For triple negative breast cancer they are looking at targeting Jak2. "In addition to targeting JAK2, there is preclinical evidence suggesting that rare mutations in HER2 may activate HER2 signaling in tumors that are HER2-negative by traditional testing. Moreover, data have indicated these patients may respond to treatment with the irreversible HER1/2-targeting kinase inhibitor neratinib."
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Next generation sequencing study finds ‘microbial profile’ may help determine time of death

Next generation sequencing study finds ‘microbial profile’ may help determine time of death | Next Generation Sequencing | Scoop.it

Using high-technology gene sequencing techniques on both bacteria and microbial eukaryotic organisms like fungi, nematodes and amoeba postmortem, the researchers were able to pinpoint time of mouse death after a 48-day period to within roughly four days. The results were even more accurate following an analysis at 34 days, correctly estimating the time of death within about three days, said Jessica Metcalf, a CU-Boulder postdoctoral researcher and first author on the study.

 

The paper on the subject was published Sept. 23, 2013, in the new online science and biomedical journal, eLIFE, a joint initiative of the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust Fund. The study was funded by the National Institute of Justice.

 

The researchers tracked microbial changes on the heads, torsos, body cavities and associated grave soil of 40 mice at eight different time points over the 48-day study. The stages after death include the “fresh” stage before decomposition, followed by “active decay” that includes bloating and subsequent body cavity rupture, followed by “advanced decay,” said Chaminade University forensic scientist David Carter, a co-author on the study.

 

“At each time point that we sampled, we saw similar microbiome patterns on the individual mice and similar biochemical changes in the grave soil,” said Laura Parfrey, a former CU-Boulder postdoctoral fellow and now a faculty member at the University of British Columbia who is a microbial and eukaryotic expert. “And although there were dramatic changes in the abundance and distribution of bacteria over the course of the study, we saw a surprising amount of consistency between individual mice microbes between the time points -- something we were hoping for.”

 

As part of the project, the researchers also charted “blooms” of a common soil-dwelling nematode well known for consuming bacterial biomass that occurred at roughly the same time on individual mice during the decay period. “The nematodes seem to be responding to increases in bacterial biomass during the early decomposition process, an interesting finding from a community ecology standpoint,” said Metcalf.

 

“This work shows that your microbiome is not just important while you’re alive,” said CU-Boulder Associate Professor Rob Knight, the corresponding study author who runs the lab where the experiments took place. “It might also be important after you're dead.”


Via Dr. Stefan Gruenwald
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Researcher Using Next-Generation Sequencing, Other New Methods to Rapidly Identify Pathogens | Lab Manager

Researcher Using Next-Generation Sequencing, Other New Methods to Rapidly Identify Pathogens | Lab Manager | Next Generation Sequencing | Scoop.it
He calls himself the bug hunter, but the target of his work consists of viruses that can only be found and identified with special methods and instruments.
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Illumina Sequencing Technology

This video provides an overview of the DNA sequencing workflow on an Illumina sequencer. The process begins with Nextera sample preparation, followed by clus...
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Diagnostic de la prochaine génération

Diagnostic de la prochaine génération | Next Generation Sequencing | Scoop.it
LabTube.tv is the online repository where you can share your scientific or biomedical videos with the wider community.
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The present and future of Next Generation Sequencing: A survey by Bio-IT World - SmartBiobank

The present and future of Next Generation Sequencing: A survey by Bio-IT World - SmartBiobank | Next Generation Sequencing | Scoop.it
Next Generation Sequencing enables scientists to obtain a deep insight on the genome, transcriptome and epigenome of various species and has become a common procedure in various areas of life science research. In October 2013, Bio-IT World conducted a survey in the biotechnology and pharmaceutical industry to obtain an insight on the latest technologies used... Read More
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All About Next Generation Sequencing | Brain Cancer Treatment Center

The field of genetics has witnessed revolutionary new technologies and trends in the last decade. One of the groundbreaking breakthroughs is the next
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Integrating Pathology and Next-Gen Sequencing for a Robust and Practical Workflow - YouTube

Next-generation sequencing (NGS) technologies have provided invaluable research tools for determining the genetic basis of disease. Enhanced genetic analyses...
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