General Business – Next Generation Technologist

Exponential technologies and electronic DNA detection

March 14, 2017 by Dale Yuzuki

We are living in a world of exponential technologies, and genomics is one of several where expectations are not set at something 30% better or cheaper or faster, but 300% within the space of a few years. The term ‘exponential’ is starting to gain traction in the general public; here in the Washington DC area … Read more

Complete human diplotypes & Google X Life Sciences podcast

April 1, 2015 by Dale Yuzuki

Theral Timpson produces a weekly podcast at Mendelspod.com, and in his latest edition he interviews me about Google X Life Sciences (I wrote about them before here), long-read sequencing (in particular Pacific Biosciences) which then I’m able to discuss the value of complete human diploid sequencing, and my involvement with the Behind the Bench blog. … Read more

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).

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.

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.

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.

A Revolution in Prenatal Diagnostics

August 19, 2012August 2, 2012 by Dale Yuzuki

Infant — Photo courtesy of <a href=”http://www.flickr.com/photos/o5com/”>o5com</a> via Flickr.

Every mother-to-be who has what is considered an ‘at-risk’ pregnancy is informed of the risks to the fetus of a genetic abnormality. ‘At-risk’ can involve a long list of medical conditions (diabetes or cancer for example) or poor health choices (illegal drug use or smoking). Yet a common cause of an at-risk pregnancy is age, having a child before the age of 17 or older than 35. In the US, no less than 750,000 are considered at-risk.

NanoString and Focused Gene Expression

August 19, 2012July 23, 2012 by Dale Yuzuki

Gene Expression Phylogenic Map — Image courtesy of <a href=”http://www.flickr.com/photos/libertasacademica/”>Libertas Academica</a> via Flickr

NanoString is a startup company that has commercialized a product called the nCounter™ system. It is able to take an RNA sample and look at the expression level of up to 800 genes per sample, and recent news indicates that it is in current preparation for an IPO.

Oxford Nanopore, the first nanopore-based sequencing technology

July 2, 2012 by Dale Yuzuki

Oxford Nanopore illustration — Image from {a href=”http://www.nanoporetech.com”}Oxford Nanopore{/a}

Oxford Nanopore, based in Oxford U.K., made a remarkable announcement that surprised many in February’s AGBT meeting in Marco Island. A GridION and MiniION single-molecule sequencers were announced, promising 15 minute runtimes, no sample preparation, and a disposable USB-stick sequencer for $900 (in the case of the MiniION), with 50kb long readlengths (and 100kb promised) at only a 4% error rate it appears to be a dream come true for many research challenges that await.

Helicos Single Molecule Sequencing – A Pioneer

June 25, 2012 by Dale Yuzuki

The next-generation sequencing market continues its downward trajectory – routinely violating Moore’s Law by an estimated 3x, the cost per megabase curve started to significantly bend downward around 2007 when the Solexa 1G started selling in volume, and gave the 454 GS20 (as it was known then) the first competition for massively parallel sequencing the market had seen.