Next Gen Sequencing – Page 6 – Next Generation Technologist

Oxford Nanopore at AGBT 2014

February 19, 2014February 17, 2014 by Dale Yuzuki

Borrowed from a Oxford Nanopore Video (without permission) — Borrowed from a Oxford Nanopore Video

A few attending the Advances in Genome Biology and Technology meeting in Marco Island Florida (February 12 – 15 2014) have blogged about a presentation from David Jaffe (Broad Institute), presenting the first data the next-generation sequencing community has publicly seen from Oxford Nanopore Technologies. For those not familiar with Oxford Nanopore (or ONT as I’ll refer to them), it was AGBT12 that they absolutely stunned the crowd in attendance with their announcements of both a GridION™ nanopore sequencing ‘module’, and a MinION™ USB-stick portable DNA sequencer that got a lot of press. They planned to commercialize ‘by the end of the year’ (that is, 2012), and since I was not there ‘in’ the meeting first-hand (I was supporting the meeting on-site at Marco Island for Life Technologies, just not as a conference attendee), I heard first-hand from several that year with interest.

Post-AGBT 2014 Thoughts & Jeffrey Schloss’ Plenary Talk (NHGRI)

February 16, 2014 by Dale Yuzuki

140217 AGBT (View from the hotel) Today (February 17, 2014) marks the end of the 2014 Advances in Genome Biology and Technology, an annual gathering whose principals include Dr. Eric Green (Director of the National Human Genome Research Institute) and Dr. Elaine Mardis (co-director, with Rick Wilson, of the Washington University Genome Institute). Every year they line up a great roster of engaging and interesting speakers (here’s the agenda for the meeting) and I thought I take a few moments to share some of the highlights from one talk.

I know there are many who want to hear about all the latest technology, and certainly there was a lot of new technology on display that I’ll write about over the next few weeks, including the latest from (in no particular order) Oxford Nanotechnology, Gencell Bio (and their remarkable CLiC™ liquid handler), and Nabsys a single-molecule genomic mapping instrument. (Some others to tease you with are the latest target enrichment from WaferGen, PacBio’s excellent showing with their new C5-P3 chemistry, and other technology such as quantum-tunneling based sequencing and using droplet digital PCR for haplotype phasing – I’m getting ahead of myself though.)

FDA Approval for the MiSeq

November 26, 2013 by Dale Yuzuki

For Research Use Only Congratulations are in order to the US Food and Drug Administration for approving the Illumina MiSeqDx™ system, including two Cystic Fibrosis assays, and two additional approvals for the platform (the instrument and the reagents). This is the first next-generation sequencer approved by the FDA, an important milestone reflecting a sea-change in how genetics and genomics is revolutionizing healthcare. The genetics revolution has been taking place for some time now – here’s a handy FDA table of over 200 pharmacogenomic biomarkers in drug labeling – but with the advent of NGS the ability to determine multiple biomarker genes via a simple electronic query is only one of several promising applications with direct clinical impact and utility.

Personal Genomics and the Future of Healthcare

November 18, 2013 by Dale Yuzuki

“The future is already here – it is just not very evenly distributed.” William Gibson, author of Neuromancer and the person who coined the term ‘cyberspace’. Way back in 2006 or so when I was working for Illumina, the personal genetics firm 23andMe launched their whole-genome genotyping service (called ‘Genetic Testing for Health, Disease and Ancestry’ … Read more

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.