Marketing

The Ion Torrent Proton at Ion World

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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.

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A busy tradeshow season and 1 in a million PCR sensitivity

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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.)

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The end in sight for Complete Genomics by merging with BGI

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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.

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BioNano Genomics, OpGen and Copy Number Variation

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Image courtesy Flickr user <a href=”http://www.flickr.com/photos/48677280@N00/”>karen2754</a>.

A few weeks ago this paper appeared in Nature Biotechnology, “Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly”. It was the first publication of a startup company in San Diego called BioNano Genomics.

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NanoString and Focused Gene Expression

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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.

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Complete Genomics’ Long Fragment Read Technology and Haplotype Phasing

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Image courtesy {a href=”http://www.flickr.com/photos/arenamontanus/”}arenamontanus{/a} via Flickr

This week a remarkable paper was published in Nature, called “Accurate  whole-genome sequencing and haplotyping from 10 to 20 human cells”. What makes it remarkable is the ability of this method to obtain rare variant phase information by changing the library preparation method. Until now to obtain completely phased individual genomes required a fair amount of laboratory manipulation.

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An Overview of NGS Targeted Selection Methods and Marketplace

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targeted selection methods and marketplace illustration
Photo courtesy of user {a href=”http://www.flickr.com/photos/vizzzual-dot-com/”}viZZZual.com{/a} via Flickr.

Although the whole genome versus whole exome discussion was held previously, details around the methods of selecting out the whole exome have been not discussed (also called ‘targeted selection’), and the wide array of methods, costs, and effort required can be a rather complicated affair.

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Single Molecule Sequencing – Pacific Biosciences and their method

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Image of Pacific Biosciences’ sequencing data, courtesy of a {a href=”http://investor.pacificbiosciences.com/events.cfm”}PacBio{/a} investor presentation.

In previous posts I covered the basics of next-generation sequencing – library preparation, template preparation, and the sequencing methodology itself, whether by pyrophosphate detection, single base extension with reversible terminators, or probe addition by ligation. And single molecule sequencing’s attractiveness as a technology has been covered here, but here I’ll detail how the startup Pacific Biosciences does it’s magic. (For some additional commentary on the company and its prospects check here.)

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Error, alignment, and the myth of the complete genome

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Centaur by {a href=”http://www.flickr.com/photos/consciousvision/”}JustMN{/a} via Flickr.

The myth of the complete genome is something that is not commonly known to active observers of genomic technologies. (The term ‘active observer’ is from the point of view of one with varying degrees of background in the biological sciences, and is in noway an aspersion.) The ‘first draft’ of the human genome was announced at a Clinton-era press conference on June 26, 2000, and it was an agreement between the two famously competitive individuals (Francis Collins and Craig Venter) representing the public (NIH and DOE) effort and the private one (Celera). This first draft was exactly that – about 90% complete, and the completed version was declared in 2003. This is not to discount the first seminal publications of this draft, as in 2001 when these papers were published (in Science and Nature respectively) the largest previously sequenced genome was 1/25th the size. In other words, the human genome represented a 25-fold leap in size and complexity of anything done to-date.

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The whole-exome vs. whole-genome sequencing debate

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By Sarah Kusala via {a href="http://commons.wikimedia.org/wiki/File:In_solution_capture.png"}Wikimedia Commons{/a}

An enterprising salesperson from Complete Genomics used this newfangled social media thing called LinkedIn to make her mark on the world (perhaps) by posing a discussion question. (It was over at the ‘Genome Interpretation‘ group in case you were wondering.) Entitled, “The last days of exome sequencing“, she posed the question whether exome sequencing day’s were numbered.

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My notes from George Church’s plenary talk at ABRF 2012

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Image via {a href="http://commons.wikimedia.org/wiki/File:George_Church_at_TED.jpg"}Wikimedia Commons.{/a}

One of the great privileges of working on the marketing side of a life sciences company (compared to the sales side) is the ability to go to a lot of conferences. As a sales representative, it was a hit-or-miss affair, whether I’d be one of the ‘chosen ones’ to go to AGBT, ASHG (now called ICHG), or ABRF.

(For those who are not in genomics, AGBT = Advances in Genome Biology and Technology; ASHG = American Society for Human Genetics; ABRF = Association of Biomolecular Resource Facilities.)

And for a sales rep, it’s a difficult task; you encounter potential customers from many quarters, increasing the sales footprint for the company as a whole, but not so rewarding for your own particular territory. On top of that, you can’t participate in the science per-se, but certainly will have other opportunities to interact with the conference attendees, and glean some of the ‘take-home’ lessons second-hand, if they are so inclined to ask.

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Four online resources for a healthy NGS information diet

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Image courtesy Flikr's {a href="http://www.flickr.com/photos/elena_norbiato/2444950911/sizes/z/in/photostream/"}Trellina{/a}

Any healthy diet has a good balance: regular ‘staples’, a fair amount of variety, and the occassional surprise ‘treat’.

For next-generation sequencing, the web offers unparalled information to keep up-to-date. Here is a short list of four sites that compose a healthy NGS diet – everyday staples and a lot of variety!

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