Next Generation Technologist

Next Generation Sequencing, Marketing, and the Genomic Revolution

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 →

February 17, 2014
by Dale Yuzuki

Oxford Nanopore at AGBT 2014

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. Continue Reading →

February 16, 2014
by Dale Yuzuki

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

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.) Continue Reading →

November 26, 2013
by Dale Yuzuki

FDA Approval for the MiSeq

For Research Use OnlyCongratulations 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. Continue Reading →

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