Dale Yuzuki – Page 10 – Next Generation Technologist

Single molecule in-situ RNA startup Advanced Cell Diagnostics

January 28, 2013 by Dale Yuzuki

Biopsy of skin sample courtesy of euthman via Flickr

FFPE (Formalin-fixed paraffin embedded) tissues are standard preparations in the clinical world. It has been estimated that there are millions of FFPE samples stored in countless hospital laboratories and research pathology groups, all part of a standard operating procedure among pathologists and other hospital personnel. These tissue samples are embedded in paraffin blocks for indefinite room-temperature storage and are easily handled, and standard staining and microscopy techniques can then be employed to determine cancer stage, for example.

Moleculo and Haplotype Phasing

January 25, 2013January 25, 2013 by Dale Yuzuki

Moleculo Man (not really) — A picture of a robot toy (sorry, my kids do not have a toy that looks like the ‘Moleculo Man’ of Conan OBrien from 2001…)

A few weeks ago at the J.P. Morgan Healthcare Summit in San Francisco, Illumina announced that they acquired a startup company called Moleculo that provides virtual long reads of 8 to 10kb. Single molecule sequencing will provide long reads (Pacific Bioscience’s RS will now go out to 5kb, although the platform is hampered by poor accuracy), and I’ve written before about last summer’s accomplishment by Complete Genomics in publishing their Long Fragment Read technology of phased reads on the order of 100kb. (And do take a look there to see why haplotype phasing is important.)

RNA-Seq and Exome Sequencing webinar presentation

November 19, 2012 by Dale Yuzuki

Hello everyone, this post is made while I’m officially on vacation, so while I may post later this week it will only be for recreational purposes. 🙂 I plan to hold two different webinars at three different occasions this upcoming November 28, 29 and 30, 2012 for any interested in RNA-Seq and Exome sequencing. I’ll … Read more

Single molecule mapping OpGen making slow progress

November 16, 2012 by Dale Yuzuki

OpGen Mapping Card — Photo of an OpGen mapping card

In contrast to BioNano Genomics, who is starting commercialization with early access customers now and full commercial launch in the Spring of 2013, OpGen launched the Argus™ Optical Mapping system in the summer of 2010. Their customers use this system for microbial strain mapping, mainly for infectious disease research or finishing reference bacterial strains.

BioNano Genomics explores Copy Number Variation

November 12, 2012 by Dale Yuzuki

BioNano Genomics Irys System at ASHG 2012 — The Irys system in the BioNano Genomics booth. Note the small chips in the lower right corner, about 3″ square, with three input/output ports to accommodate three samples.

ASHG 2012 in San Francisco is finally over! The exhibit booths get torn down, the equipment gets packed up and shipped to storage, and hundreds of foot-weary front-line soldiers get back to their normal routines, whether in sales, marketing, product development, R&D or product management.

Oxford Nanopore and commercialization at ASHG 2012

November 9, 2012 by Dale Yuzuki

Oxford Nanopore at ASHG 2012 — Clive Brown (left) showing the minION at their ASHG 2012 booth. Matthew Hickenbotham, colleague at Life Technologies, at right.

Here at ASHG 2012 in San Francisco this week, a ton of activity around the exhibitors, and Life Technologies does not disappoint with the Ion Bus on the show floor, an open 20 foot x 30 foot booth, a new digital PCR instrument (the QuantStudio 3D) introduced, two luncheon workshops, an Ion Torrent User Group meeting, a special SF Museum of Modern Art event on one evening, and an Ion Lounge evening event on the other. (These last two events were described internally as ‘networking only’, which is a code-word for a great social event.)

Readlengths do matter in Next Generation Sequencing

October 8, 2012 by Dale Yuzuki

Length Matters Notebook cover — Notebook cover from AGBT 2009 (c) Dale Yuzuki

Recently I was asked about how important readlengths are, in the context of where MiSeq and Ion Torrent PGM currently stand in the marketplace. As the 454 advertisement used to say until recently, ‘Length Matters’. Given a number of recent announcements from Ion Torrent and the other folks in San Diego, let’s assess where we are.

The Ion Torrent Proton at Ion World

October 1, 2012 by Dale Yuzuki

Chad Nusbaum at Ion World 2012 — Screen capture of Chad Nusbaum, courtesy of YouTube.

Product launches are exciting things, and the Ion Torrent Proton has officially launched (as of the recent Ion World conference September 13-14, 2012). For those who were not able to make it to San Francisco for that two-day event, we now have the videos of four presentations up on the Ion Torrent YouTube channel, and for those who have complained about the ‘lack of data from the Ion Proton’ there’s quite a lot of ground to cover, and there’s a fair amount of interesting items about the PGM too. The Ion World-specific list of videos are linked here on an Ion Torrent Community page for ease of reference.

A busy tradeshow season and 1 in a million PCR sensitivity

September 28, 2012 by Dale Yuzuki

TradeBooth — Image courtesy of philmanker via Flikr.

Attending any conference as a vendor is a busy time. Anyone who works in the life sciences vendor segment in commercial (i.e. customer-facing) marketing will understand that traveling to a few tradeshows in a year is a part of the job, and often an enjoyable part of the job at that. (Imagine a company-paid expensive hotel in a cosmopolitan North American or European city’s downtown nightlife district, early-morning through late-night activity that may include a nice dinner, company social events for customers and prospects, being on your feet in a 10-foot tradeshow booth engaging customers and prospects in real-time, sharing and receiving information in a constant stream in a time-limited way, and you get the general idea.)

Is there room for 90 providers of genomics software?

September 24, 2012September 23, 2012 by Dale Yuzuki

Alignment_File_Figure — Image courtesy Libertas Academica via Flickr.

“Let a hundred flowers bloom, let a hundred schools of thought contend”, Mao once said during the Revolutionary Days of 1957. Now in the middle of a genomics revolution, it feels that way in the market for genomics software to analyze next-generation sequencing data. New companies are being formed, large software and hardware firms are expanding into the life sciences, and others are offering in addition to software options the implementation of a cloud-based service.

The end in sight for Complete Genomics by merging with BGI

September 17, 2012 by Dale Yuzuki

Complete Genomics was started in 2005 with the promise of setting up a whole-genome sequencing service for millions of human genomes at a very low cost. Launching a service in 2009 at $5,000 per individual sample, Complete Genomics went public under the symbol GNOM in November of 2010 at $7.69/share, reaching a high of $17.42 in June 2011 before returning to it’s IPO price in Sept 2011, and then declining to the $2 to $4 range.

The Ion Chef, Avalanche, and a 1.2 B sensor PIII chip

October 14, 2012September 14, 2012 by Dale Yuzuki

Jonathan Rothberg and the Ion Chef — Jonathan Rothberg showing off the just-announced Ion Chef for automated library creation, template preparation and chip loading

A Life Technologies-sponsored 2-day conference called Ion World 2012 kicked off yesterday afternoon, with Jonathan Rothberg founder of Ion Torrent, Tim Triche of the Childrens Hospital of Los Angeles, Joe Boland of the Division of Cancer Epidemiology and Genetics at the National Cancer Institute, Shawn Levy of Hudson-Alpha Biotechnology Institute, and Craig Venter from Synthetic Genomics and the J. Craig Venter Institute all speaking.