Next Generation Technologist

Next Generation Sequencing, Marketing, and the Genomic Revolution

March 10, 2014
by Dale Yuzuki

The upcoming Proton PII and the NextSeq 500

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

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. Continue Reading →

March 3, 2014
by Dale Yuzuki

Nabsys single molecule mapping technology

Close-up of Nabsys ChipAnother 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). Continue Reading →

February 24, 2014
by Dale Yuzuki
1 Comment

Targeted RNA Sequencing Approaches

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? Continue Reading →

February 20, 2014
by Dale Yuzuki
1 Comment

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

Standing in front of the CLiC LP at AGBT

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). Continue Reading →

February 19, 2014
by Dale Yuzuki

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

The LifeTech Variant Detective Showcase at AGBTA 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. Continue Reading →

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