Wednesday, 30 November 2011

BGI Team Developing 'All-in-One' Capture Technique

Just a quick re-post from another blog (InSequence, GenomeWeb). This one is an interesting effort by the BGI to go beyond the exome in target sequencing.

BGI Team Developing 'All-in-One' Capture Technique to Go Beyond the Exome | In Sequence | Sequencing | GenomeWeb

Much more than a single Personal Genome

With sequencing costs rapidly falling down, the era of personal genomics seems at hand. Soon we can analyze the entire genome of an individual for a bunch of dollars and know everything about its genetic predispositions...But someone says it's no time for easy celebrations, since che scenario is far more complex than usually believed: in his recent post John Rennie at Smart Plant's Savvy Scientist, underlines that actually we have more than one personal genomes and we have to take all these ones in to account in the future. An intriguing example is the fact that specific genomic rearrangements occur frequently in single neuronal cells in mammals, increasing the complexity, flexibility and responsivness of neuron networks and they may play a role in various psichiatric and neurodegenrative disorders. Togheter with other already known phenomenon such as mosaicism and chimerism and the increasing relevance given to mictobiome in human biology and pathology, it really makes no sense to talk about a single Personal Genome...We are dealing with a GROUP of Personal Genomes...Lets sequence them all!

Ion Torrent: a "robust" technology

Ion Torrent Personal Genome Machine (PGM) is one of the most promising and innovative instruments in the field of Next Generation Sequencing. The revolutionary method based on ion release and semiconductor technology make the Ion Torrent machine a member (as we are likely going to use one PGM, we hope the best member) of the non-optical based sequencers group. Little is known about its potential, but despite its young age, Ion Torrent showed its muscles in different efforts such as the sequencing of E. coli O104:H4 genome, responsible of the outbreak of foodborne illness focused in northern Germany in spring 2011.
On October 25th we attended in Verona the "User experience tour" organized by Life Technologies to share the experiences of research groups that are already using the Ion Torrent PGM. More than 40 cities around Europe were connected in video conference with the main event in Berlin opened by the welcome of Jonathan Rothberg, Founder and CEO of Ion Torrent. To the organizers who thanked him for being connected at 6 am from US Rothberg answered "I wake up every day at 5 o'clock to make this technology easier and faster". Three different sessions were organized, ranging from Bacterial Sequencing to Target Resequencing and RNA-Seq techniques. At the end of the day the general impression was that PGM is a quite impressive machine with a promising future potential that also rely on the contribution of the user community. We appreciate this open-source attitude and we hope to be able to contribute as soon as possible!.

P.S. before leaving, the organizers gave us a 316 chip (already used) as a gift. Back to the lab, we thought to create a fancy keychain with it. We tried to make a hole in the chip with a drill but, except for the plastic surface, we couldn't make even a scratch on it! The least we can say is that it's a really "robust" technology!!

Just a couple of interesting tools

Look around for smart tools useful to safely walk through the NGS field I found these interesting pieces of research:

GenomeView: a next-generation genome browser
This seems a really good browser to visualize data from NGS. It can visualize the millions of reads produced by your sequencer as well as an entire genome aligned to your reference. Citing the authors: "GenomeView is unique in its capability to interactively handle huge data sets consisting of tens of aligned genomes, thousands of annotation features and millions of mapped short reads both as viewer and editor." Even more GenomeView is freely available as an open source software package.

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome
Sharing effort in target capturing is a really promising solution to reduce the costs of target enrichment, that are emerging as a real bottleneck in most NGS applications. Again lets talk the authors: "In total, this resource provides 92.1% in silicocoverage of the human genome. The online server allows researchers to download a complete repository of oligonucleotide probes and design customized capture assays to target multiple regions throughout the human genome."

Tuesday, 29 November 2011

If you don't believe in Zone Diet you may try with miRNA diet

In a recent paper appeared on Cell Research, authors found that miRNA assumed with diet (particularly with eaten plants) can be found in the blood stream of the eating animals. Some of them can also influence human physiology as in the case of miRNA168a that inhibit LDL removal by the liver.
This suggests a new class of molecule as key components in the diet and open new scenarios for evolutionary processes with diet playing an even more important role, as commented in Scientific American.

So the next time you search for those healty foods, be sure to check for miRNA!