Dale Yuzuki – Page 9 – Next Generation Technologist

Update from BioNano Genomics at #ASHG2013

November 1, 2013October 31, 2013 by Dale Yuzuki

BioNanoGenomics' chip, shown at ASHG Boston 2013 — BioNanoGenomics‘ chip, shown at ASHG Boston 2013

Almost a year ago I wrote up this post about a startup called BioNano Genomics, which was hard at work launching a nanofluidic device and scanner called the Irys™. At February’s AGBT meeting in Marco Island (FL), they presented a scientific poster about the spider mite genome. Tetranychus urticae has a lot of interesting features, including being an important agricultural pest. Now I don’t have anything against entomology per-se, it is just that the capacity of a genetic analysis system will need to look at humans (at 3 gigabases for the haploid genome), rather than insects (T. urticae is on the order of 90 megabases, and today I learn that it is the smallest arthropod genome sequenced to-date).

Next-Generation Sequencer GnuBIO

October 28, 2013 by Dale Yuzuki

GnuBIO next generation sequencer — The GnuBIO’s new sequencer at ASHG

There are two next-generation sequencing ‘platforms’ (i.e. systems) that are being prepared for commercial launch; one from QIAGEN (that I wrote about here and I was told at ASHG that they working hard to launch it in 2014), and another from GnuBIO. This technology came out of the same laboratory that RainDance Technologies’ emulsion droplets came out of (David Weitz’ ‘squishy physics’ laboratory), and it applies the microfluidic principle to sequencing chemistry on a picoliter scale.

Formulatrix and an inexpensive digital PCR for NGS library quantitation

October 26, 2013 by Dale Yuzuki

Underside of the Formulatrix Digital PCR Plate

The American Society for Human Genetics 2013 Annual Meeting was held this week in Boston. Starting from Tuesday and going through Saturday, there are ancillary meetings both before and after (and Life Technologies had an Ion World event the two days prior). As one of the two ‘main event’ trade-show exhibits for the genomics tool-providers (the other being the Advances in Genome Biology and Technology in Marco Island FL every February), you can learn a lot by walking around and talking to different vendors.

Ion Chef, PII Chip, Isothermal Template Prep and a new Hi-Q Enzyme at Ion World 2013

October 23, 2013 by Dale Yuzuki

Over the two days right before the annual ASHG (American Society of Human Genetics) meeting in Boston, Life Technologies held a two-day event where several hundred Ion Torrent customers and other interested parties attended.

Updates for three upcoming products (the Ion Chef automated template prep, the PII chip, and a product formerly called Avalanche but is now generically named ‘Isothermal Template Prep’) were shared which were expected. A new more highly accurate sequencing polymerase was announced.

The new QuantStudio 3D™ digital PCR instrument

October 4, 2013October 4, 2013 by Dale Yuzuki

QuantStudio 3D Digital PCR System — The QuantStudio 3D, image courtesy of Life Technologies.

You may (or may not) have heard about digital PCR, which is set to be the next application set to explode in the gene expression market. But Life Technologies has a continuing investment in genetic analysis, and this new instrument, the QuantStudio 3D, demonstrates it.

The Fluidigm C1™ Single Cell Auto Prep System

September 27, 2013September 27, 2013 by Dale Yuzuki

The Fluidigm C1 single cell microfluidic chamber showing a capture — The Fluidigm C1 IFC chip, borrowed from Fluidigm’s Spec Sheet

Every human being came from a single cell. While that fact may not be so obvious in our day-to-day routine, the power of a single cell is observed with the burst of research activity in stem cells and induced pluripotent stem cells (and also see the Nobel Prize winner for 2012 in Physiology or Medicine, Shinya Yamanaka, who discovered the reprogramming process). In cancer research, the concept of cancer stem cells has developed into a major effort into identifying and characterizing circulating tumor cells (“CTC’s”) by which metastatses occurs. This was a major topic of discussion at the Spring 2013 AACR meeting in Washington DC, as well as a recent Next Generation Dx meeting (also in Washington DC). In many other areas of human disease biology, the inherently heterogeneous nature of tissues in general point to the need to analyze biology at a much finer resolution.

Ion AmpliSeq™ Exome – 294,000 primer pair PCR

July 1, 2013 by Dale Yuzuki

Ion Torrent Exome, courtesy of Life Technologies

Today Ion Torrent launches a neat product based upon a highly multiplexed technology called AmpliSeq, called the Ion AmpliSeq Exome, covering >97% of the CCDS regions. But before getting into the details, a little context is in order.

Sony, microfluidics, and a novel flow cytometer i-Cyt

April 29, 2013 by Dale Yuzuki

A photo of the Sony DADC i-Cyt microfluidic chip. The Sony SH800 is in the backgroun. — A photo of the Sony DADC i-Cyt microfluidic chip. The Sony SH800 is in the background.

It was something of a surprise to see Sony exhibit at the AACR meeting, and a bit more of a surprise to see that they have been successful in their quest to diversify out of the CD, DVD and BluRay manufacturing business.

iCyt is a company founded in Champaign Illinois, and in 2010 was acquired by Sony. They have introduced a flow cytometer and lower-end flow analyzer, and it is the flow cytometry application that at its center uses Sony-developed plasticware. Their ‘flagship’ unit (called the Cell Sorter SH800) uses at its center a disposable plastic microfluidic device pictured above.

The next NGS platform – the QIAGEN GeneReader™

April 22, 2013 by Dale Yuzuki

The QIAGEN GeneReader at AACR (April 2013)

Earlier this year at the February AGBT Conference, a person from QIAGEN came over to the Ion Torrent suite and asked me a few questions about the Ion Proton and in particular the upcoming Ion Chef unit. (The Ion Chef for those not familiar with it can replace the OneTouch 2 automated template preparation instrument with another one that will not only perform the emulsion PCR but also enrich the ion sphere particles, and load the chips as well.)

SmartFlares™ – single-molecule fluorescence of RNA in-vivo

April 16, 2013 by Dale Yuzuki

At last week’s American Association for Cancer Research (AACR) meeting in Washington D.C., it is the serendipitous discovery from walking around the exhibit hall that gets the creative thinking going. And at such a large venue – there were about 17,000 scientists in attendance – you never know what you’ll find among the 22 rows … Read more

The Ion Torrent Proton at Advances in Genome Biology and Technology AGBT

February 22, 2013 by Dale Yuzuki

Ion Torrent Bus AGBT Marco Island — The Ion Bus on the beach at AGBT Marco Island FL

This week the annual Advances in Genome Biology and Technology (AGBT) meeting is being held, as it usually is, in Marco Island Florida. As a Gulf Coast resort area complete with white sand beaches and thatched hut shade, Marco Island every February has been one of the ‘must attend’ conferences for those who want to know what the current leading-edge research techniques and methods are using next-generation sequencing. And for the vendors, it is a non-stop week of activity. (One person on Twitter called it the ‘Detroit Auto Show of Genomics’.)

Seeing shades of the future: NGS and Personalized Medicine

February 4, 2013 by Dale Yuzuki

doctor stethoscope — Photo courtesy of Alex Proimos via Flickr

In the world of NGS a sea-change is occurring, and that is the shift to clinical applications of this technology to personalized medicine. It seems like a long time ago and it was only in 2005 when the Roche / 454 GS-20 first started appearing in genomics laboratories, and 2007 when the Solexa 1G first appeared. I was involved with some of the earliest adopters of NGS into clinical genetics laboratories way going back go 2008 and 2009 – these groups were quick to realize the potential of the technology, undertaking the risk of a very fast-changing technology, with regular changes to systems, reagents, protocols and software, all of which militate against adoption into a regulated laboratory-developed test environment.