Dale Yuzuki – Page 8 – Next Generation Technologist

WaferGen SmartChip TE™ – a PCR-based approach to target enrichment

March 24, 2014March 19, 2014 by Dale Yuzuki

A WaferGen chip, finger and photo courtesy Dale Yuzuki — A WaferGen chip, photo courtesy Dale Yuzuki

WaferGen is a California Bay-Area company that originally developed an idea similar to BioTrove, which was to create a solid substrate with nanoliter-sized wells for high throughput real-time PCR. WaferGen’s SmartChip™ has 5,184 wells (that’s a 54 multiple of 96), while BioTrove’s OpenArray™ has 3,072 (that’s a 32 multiple of 96). The concept is that each well contains a real-time assay master mix and the sample of interest, and a flexible format of sample number / real-time targets (either gene expression or end-point genotyping) can be performed in a single run.

Ion Chef™ System ships to first customers

March 14, 2014March 13, 2014 by Dale Yuzuki

Ion Chef Shipments going out (photo credit to Michael Aken of Life Technologies)

Way back when I was pouring ³⁵S-labeled dNTP Sanger sequencing polyacrylamide gels (and fond memories of using reagents like degassed acrylamide, TEMED and Silane), robotic automation was at that time only in an industrial or manufacturing context. Now there are many automated liquid handling companies (for example Beckman is a popular choice, but Tecan and Hamilton and others share the market), and many options when it comes to setting up reactions in a 96-well format.

But when it comes to taking a single next-generation sequencing library molecule, affixing that molecule to a bead or particle (or in the case of a 5500xl Wildfire or Illumina flowcell) and then amplifying that molecule 1000’s or 100’s of thousands of times is not a trivial task. This is typically termed ‘template preparation’ – alternatively Illumina calls it ‘cluster generation’.

Some clarifications about Ion Torrent PII and NextSeq 500

March 11, 2014 by Dale Yuzuki

Yesterday’s Ion Torrent Proton PII™ and Illumina NextSeq 500™ post certainly got a reaction from several quarters, including detailed pricing information about the 1x75bp format for the high-throughput configuration on the consumables. Instead of making edits to the original here are some clarifying points, as it is clear that Illumina is making a break from … Read more

The upcoming Proton PII and the NextSeq 500

March 10, 2014March 10, 2014 by Dale Yuzuki

Record PI runs with a 20.5GB at the top, from the Ion Community site

There has been a lot of publicity around the NextSeq 500 from Illumina, and it appears to have been designed to compete directly against Ion Torrent’s upcoming PII chip. Thanks to a visit to upstate New York last week, I met Dr. Sridar Chittur who told me how important it was to put current information out on this blog, and if I can put out the disclaimers up-front it would be very helpful for those thinking about what benchtop system to purchase over the next several months.

Nabsys single molecule mapping technology

March 3, 2014 by Dale Yuzuki

Close-up of Nabsys Chip Another interesting single-molecule technology is a company out of Providence (RI) called Nabsys. For several years I had heard the name involved in developing single-molecule sequencing technology, and this technology will start its initial product around genomic mapping, rather than sequencing.

For background on genomic mapping and CNV analysis along with the competitive landscape, here are prior pieces written previously called BioNano Genomics, Opgen and Copy Number Variation, and an update on BioNano from last Fall’s ASHG meeting. So while BioNano Genomics and OpGen both use optical mapping of single molecules, Nabsys uses electrical detection. (Cue the optical vs. digital detection methodology of Ion Torrent here).

Targeted RNA Sequencing Approaches

February 24, 2014 by Dale Yuzuki

Happiness is getting more of what you want, in RNA-Seq as in other things... — Happiness is getting more of what you want, in RNA-Seq as in other things…

There are several commercial methods for looking at 10’s or 100’s of gene expression levels via a high throughput TaqMan™ assay from Life Technologies / Thermo Fisher Scientific, a competitive offering from Roche, Douglas Scientific, or also Fluidigm. The limitation of these technologies however is the amount of multiplexing a single assay in a given volume, which regardless of the amount of miniaturization does limit the samples by genes evaluated throughput.

To perform RNA-Seq, one looks at all the particular RNA species present, dependent upon the up-front sample preparation. (To clarify, a miRNA experiment would purify small RNAs then go into cDNA synthesis and sequencing; mature polyA+ RNA can be purified and then cDNA made and sequenced etc.) But what about a targeted set of expressed genes to evaluate via NGS?

Gen Cell Biosystems’ CLiC NGS Library liquid handler at AGBT 2014

February 20, 2014 by Dale Yuzuki

Standing in front of the CLiC LP at AGBT

One of the most interesting liquid handling technologies I’ve seen in a while was from a Limerick (Ireland) company called Gen Cell Biosystems. As a person who used to hear all about Laboratory Automation from the BioRobot™ folks in my days at QIAGEN, as well as the Society for Biomolecular Screening (SBS) also from my prior work in the protein purification and detection business (read: everything and anything about His-tagged proteins), it should not have come as a surprise that several years ago both associations merged to form the Society for Laboratory Automation and Screening (SLAS).

A favorite talk at AGBT 2014 – Gene Myers (Max Planck Dresden)

February 20, 2014February 19, 2014 by Dale Yuzuki

The LifeTech Variant Detective Showcase at AGBT A thoroughly enjoyable surprise at the Advances in Genome Biology conference last week was hearing Gene Myers of Max Planck Institute of Molecular and Cell Biology in Dresden, Germany. It wasn’t because it was about assembling a de-novo human genome at 54x coverage from a Pacific Biosciences RSII dataset in a fraction (some 1/36th) of the time, it wasn’t because of the elegance of the presentation – it was because it was for the first time in 10 years that Gene Myers attended AGBT, and for a simple reason – he did not consider short-read sequencing ‘intellectually satisfying’.

You know you are hearing from an unusually talented person when they talk about things that are intellectually satisfying.

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