next-generation sequencing

Next Generation Sequencing – Library Preparation

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Image via Flickr courtesy {a href="http://www.flickr.com/photos/ccacnorthlib/"}CCAC North Library{/a}

Looking at sequencing from one perspective, library preparation is straightforward. Sequencing a genome (whether bacterial on the order of 5 million bases or a human at 3 billion bases) is a shotgun-based affair with tens of millions to tens of billions of reads that overlap multiple times across the genome (known as ‘fold coverage’). (Thus a 30x human genome coverage would require some 90 billion bases, or a 15x coverage of each haploid allele.) Multiple random start points, 30-fold coverage across the entire genomic sample, one takes a gDNA sample, randomly shears it, attaches synthetic adapters, and off you go following the manufacturer’s protocol on getting sequence data out, whether by Roche / 454, Illumina GAIIx or HiSeq 2000, Life Technologies SOLiD or 5500xl, Pacific BioSciences RS, Illumina MiSeq, Life Technologies Ion Torrent PGM…

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Next Generation Sequencing – A Few Fundamental Concepts

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Image courtesy of {a href="http://www.flickr.com/photos/pacoseoaneperez/"}Paco Seone{/a} via Flickr

As I mentioned in my prior post, Sanger capillary sequencing is not going away anytime soon. Yet next-generation sequencing has made a huge mark in the world – growing from zero in 2005 to a USD $1 Billion market in 2012. And its growth is estimated by various sources to grow 20 to 25% every year for the next five years, approximately tripling in size from where we are now.

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Next-Generation Sequencing – its historical context

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Photo of J. Craig Venter Inst. circa 2005 by {a href="http://www.flickr.com/photos/jurvetson/"}jurvetson{/a} via Flickr.

Even though the history of next-generation sequencing is short (the 454 GS20 came out in 2005, the Solexa 1G in 2007, and the SOLiD 2 in 2008), there is a robust genomic revolution going on, and a fierce battle in the marketplace with plummeting costs and soaring throughput. Whether Moore’s Law is beat by some 2.5-fold or even faster, there is no question that we are in the middle of burgeoning growth, remarkable discovery, and new insights and discoveries just about every day.

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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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Some thoughts on Pacific Biosciences single-molecule sequencing

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SMRTcell of a PacBio RS system courtesy of {a href="http://www.flickr.com/photos/konradfoerstner/"}konradfoerstner<{/a}.

We’re living through a time this year of market transition. The Illumina HiSeq continues to have a strong market position (although the upcoming Ion Torrent Proton sets out to change that, however it won’t be available until this September / October). For the time being, customers with NGS platforms are considering upgrading (from the HiSeq 2000 to a ‘fast-mode’ 2500, or from a 5500 to a 5500 ‘Wildfire’ that will be launched later this year, decreasing the cost-per-base substantially and eliminating ePCR).

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What is a new Next Generation Sequencing customer to do?

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Photo via Flickr by {a href="http://www.flickr.com/photos/rwp-roger/"}antwerpenR{/a}

In the roads I travel (and it is now over six years since I made that fateful move from being an ‘internal’ Product Manager to ‘customer-facing’ sales representative) the buying process is all about perceptions of the customer. Right or wrong, potential customers each receive the information from a local representative (from whichever vendor) and filter it through their own set of criteria. Opinions they read in their journals of choice, opinions from their valued collaborators and other friends in the research world, tidbits gathered from their post-docs, all form a perception in their mind about what a particular product’s value is to them.

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Sequencing equipment provider Pacific Biosciences (PACB) and the rate of change

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Pacific BioSciences RS Sequencer, from their {a href="http://www.pacificbiosciences.com/news_and_events/mediakit"}media kit{/a} page.

February 2008, Marco Island Florida – an exciting time in the world of NGS, the first pioneering papers were being published using short-read sequencing that are now every-day applications – ChIP, RNA-Seq, small RNA, the first whole genomes.
 

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High School biology students and Genomics

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Santa Monica High School - ah the memories! (via {a href="http://commons.wikimedia.org/wiki/Main_Page"}Wikimedia Commons{/a})

Over the past few years I’ve been interested in contributing back to the community I live in, but as a busy father-of-three (ages 3 to 9) there just isn’t the ability to ‘cold-call’ a local high-school and volunteer.

That is, until a family vacation took us to Colonial Williamsburg VA and a tour of the Governor’s Mansion. There was a person there with a ‘Wootton Patriots’ T-shirt, and, well, as Newsweek indicated it was one of the country’s top 100 high schools in their 2010 ranking, I thought I’d speak up and ask if he happened to be involved with the local high school.

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Just what is “Next Generation Technologist” about anyway?

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Photo courtesy of {a href="http://www.flickr.com/photos/mknowles/"}mknowles{/a} via Flickr

“The future is already here – it’s just not very evenly distributed.” – William Gibson

This is a blog about next-generation sequencing and it’s intersection with marketing and business in general (primarily), which happens to be my particular area of professional expertise, having focused on next-generation sequencing since late 2006, when Illumina (my then-employer) acquired a startup called Solexa for $417M. I have had product development, product management, marketing (all in the San Diego area with Illumina) and key-account sales roles (in the Mid-Atlantic region of the US serving both the NIH and the entire SouthEast region with Illumina, RainDance Technologies and currently with Life Technologies). I am presently in a marketing role at Life Technologies Corporation (which used to be Applied Biosystems and Invitrogen Corporation), heavily involved with both the Ion Torrent PGM / Proton as well as the SOLiD / 5500 platforms. (More information about me can be found here; if you are interested in anything Ion Torrent and NGS market overall you’ve come to the right place.)

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