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.
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.
Grégory Meunier's insight:
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.
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.
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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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.
"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."
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.”
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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