Omics! Omics!

The Challenges of Sequencer Comparison

2012-05-14T21:26:00.000-04:00

I've slipped back into a lack of posting again. Some of it is a residual from my recovery this spring from surgery (physical therapy can really be draining), and a lot is due to being really busy in the day job (finding highly rare substances like dilithium is not easy), but in the end those are incomplete explanations. What should be really embarrassing is that I got access to Nick Loman and colleagues' comparison of benchtop sequencers several days before it published, and here it is weeks later and I'm finally getting around to covering it.

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Thank You, Mrs. Woodrow

2012-04-04T22:50:00.000-04:00

Tonight I will continue the recent trend of punching these out on some magical date. Now, I usually have some sorry excuses for my erratic writing, but for once I actually have something bordering on reasonable. Just after writing about Oxford Nanopore, my confidence in my skiing skills exceeded my actual skills, resulting in my femur taking on my tibia. Here for sure, size matters, and the tibia lost horribly..

Announcing the Omics! Omics! Sequencer Evaluation Program

2012-04-01T22:32:00.000-04:00

A serious issue which has been raised often both by myself and commenters is the challenge of properly evaluating sequencer performance prior to widespread commercial availability of a platform. A number of roads have been frequently taken, but each have their issues. Data generated by a company is always met with suspicion. Alpha releases are often to academics connected to a company, which has the advantage that they are likely the most passionate about proving its worth, but the downside these users may not be viewed as fully objective. Beta (or early release) sites are often less connected to a company, but by the time they publish their results through peer-reviewed journals it is long since commercial launch. Conferences such as Marco Island help shorten the cycle time, but not entirely. Early users are sometimes also suspected of having agreements which give the platform makers the power to squash bad data. So how can a manufacturer gain "street cred" for their instrument

An Oscar Night Request

2012-02-26T21:28:00.000-05:00

I've tried pretty hard to keep this blog focused on all the omics, but occasionally take the license to stray to my other interests, primarily one of them. Tonight is the Oscars, and I have a plea for the movie industry. Now, I realize the overlap between readership of this space and the big wigs in Hollywood is tiny, but perhaps a friend-of-a-cousin-of-a-spouse-of-a-sibling of a reader can make a difference. It is this simple: you have less than two years to get off your rears and launch a Blu-Ray 30th anniversary edition of an Oscar-winning picture.
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Why Oxford Nanopore Needs to Release Some Data Pronto (Besides Bailing Me Out)

2012-02-24T21:12:00.000-05:00

Last week's piece on Oxford Nanopore got a lot of attention and a lot of comments, which to me is the true mark of success in this space (discounting the higher than normal spam attempts). A couple of folks were kind enough to tweet a link (now captured in Nick Loman's wonderful tweet archives for AGBT 2012), and it was also picked up by Matthew Herper at Forbes, Dan Kobolt at MassGenomics and others (apologies for all I haven't shouted out). It also can't be denied that some of those comments felt I had been too generous / gullible with Oxford Nanopore

Oxford Nanopore Doesn't Disappoint

2012-02-17T12:01:00.218-05:00

Oxford Nanopore's AGBT presentation should have just finished up, so the embargo is off. Oxford was kind enough to chat with me last night and to share their press release in advance; on the call were CTO Clive Brown, SAB member Ewan Birney and Director of Communications Zoe McDougall. A real challenge posed by Oxford's news is trying to write about it without slipping into clichéd techspeak about what they will be releasing later this year ("second half").

2012: Enter the Nanopores?

2012-02-06T23:03:00.000-05:00

This summer will make it twenty years since I first heard of the concept of nanopore sequencing. A very affable post-doc in George Church's lab was starting some experiments in the concept. Unbeknownst to any of us, another group at Harvard in the Biolabs (Dan Branton's) was also working on a nanopore sequencing technology. In the time since then, the field has generated many papers and much speculation, but no workable sequencer. I had started joking a few years ago that nanopores were the monorails of sequencing: always the technology of the future. To be a bit more fair, nanopores had started to resemble nuclear fusion, a tantalizing vision always just out of technological reach.

Does Illlmina Also Have A Homopolymer Problem?

2012-01-30T23:38:00.001-05:00

One of the most widely-publicized error modes with Ion Torrent and 454 sequencing has been the challenge of correctly counting the number of bases in homopolymer runs. Because these chemistries use non-terminating nucleotides, polymerase is free to add as many as possible. Unfortunately, the signal linearity breaks down, making it difficult to correctly count. Ion Torrent today released a note on homopolymers, but rather than plowing this well-trod ground it goes for a less publicized problem: Illumina having a more specific challenge in this department. The note is available on the Ion Community, free registration required.

Roche Guns For Illumina

2012-01-25T23:16:00.000-05:00

Due to a business dinner & general exhaustion, I turned in early last night & was caught unaware this morning of the big news: Roche is making a hostile takeover bid for Illumina. Ugh!
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Sequencing Technology Fireworks

2012-01-10T22:52:00.000-05:00

I actually awoke today expecting an exciting press release, but I sure wasn't prepared for the big announcements from Ion and Illumina. Not that they were totally unexpected, but there's a huge difference between speculation and announced products (which, of course, are hugely different from ones you can actually buy!)

Ion Torrent Pairs: To What End?

2012-01-07T23:13:00.000-05:00

Ion Torrent quietly released a set of paired end datasets over the holiday break. This is a bit embarassing for me, as in my last post on Ion I stated the platform "will probably never have paired ends" and in fact Ion had already announced the protocol. Oy! I also missed their mate pair protocol being released, though the document itself is another victim of Ion's incredibly counterproductive security policy. If you don't own a PGM, you can't access the document -- never mind if you are trying to plan for a potential buy or are preparing a library for a friend/collaborator to run.

Year's End

2011-12-28T13:10:00.000-05:00

I hoped this year to push myself to blog more frequently and regularly. Clearly I did better than some years, but not up to the standard I had hoped for. I've also realized that I missed noting some significant personal milestones.

Reflecting on a Year of Ion Torrent

2011-12-09T08:46:00.001-05:00

Ion Torrent released three more datasets this morning, all generated on their 318 chip. One's from E.coli but two are human genomic samples. With approximately 1.2Gbp of raw data coming from these 318 chips (fron around 6 million quality filtered reads per chip), they are starting to move up the food chain in human genomics from pure amplicon sequencing to more complex small targeted resequencing efforts.

Fitting Out

2011-10-27T08:37:00.000-04:00

One of the attractions of my new shop was the possibility to see a biotech company built from the ground up. Each of my previous companies had been a long-standing concern by the time I got there; even Codon Devices had a year plus under its belt and some equipment already mothballed. The new venture moved into its first lab space last week, and as you can see from the picture all we have at the moment there are bare walls.

MiSeq Made Easy?

2011-10-11T06:01:00.001-04:00

The first computer I ever tried to program was built from a kit by my brother and father. The DATAC-1000 was a single-board machine, with that single printed circuit board about the area of a large laptop (image on page 9). Sporting a grand 1K of RAM, it was a grand machine. User input-output was entirely through a set of binary touchpads and LEDs, though a cassette tape interface enabled storing and reading programs. If I helped any with it, I might have sorted the resistors since I had just learned the color code. The machine sported the same processor as some other machines of the time, such as the KIM-1 and the PET and even something called an Apple.
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Thinking Outside the Box or Just Plain Nuts?

2011-09-28T23:52:00.000-04:00

Please take the title in the spirit it is intended: as a bit lighthearted. Seeing the object pictured and reading the accompanying blog post from one of Jonathan Eisen's graduate students. It's an unusual solution to a common problem, and gave me a good chuckle.

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Boston's Boris Bikes

2011-09-27T21:52:00.000-04:00

When I discovered that my new gig would temporarily in Boston, I realized I had an opportunity to try out Boston's new bikeshare program. Started this summer, Hubway consists of racks of bikes in public places which can be used for short hops around town. I like my folding bike, but on some rush hour trains it is very hard to find space for it, especially with some train conductors who are more interested in giving dirty looks than serving their passengers. Plus, it's now quite dark on the last leg of my commute, and even if I had some really slick lights I don't like riding even short distances in the dark.

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Transitions

2011-09-18T21:55:00.000-04:00

I went to an Infinity going-away lunch last week. We head off to some favorite local restaurant and order a modest (but delicious) meal on the company dime. The departee makes an impromptu speech, there are goodbyes and handshakes and usually a number of pleas to stay, both fictitious and heartfelt. Those staying wonder what could lure someone away from the very safe and green pastures of the company. I've been to many such lunches with Millennium and Infinity; with Codon the lunches tended to be group affairs as people were laid off in batches.

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Illumina Calls for a Flag on the Play

2011-09-14T09:10:00.001-04:00

Continuing my sports analogies, but switching games, in my coverage of the benchtop sequencer war today. Alas, I can't refer to instant replay, as the usual set of procrastination excuses has resulted in this being filed very late after I was made aware of it (first by a comment in the blog, then by a friendly chap from Illumina alerting me). In any case, Illumina has responded to Ion Torrent's claims on long reads and overestimated MiSeq quality, and mostly done so by crying "Foul!".
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Genetic Education:

2011-09-01T08:30:00.093-04:00

A study by the American Society of Human Genetics (ASHG) is published today suggesting that few U.S. states have adequate standards in place for genetics education. I forgot to ask for a link to the article that would go live post-embargo, but it should be on the website of the journal (CBE Life Sciences Education)

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Will Max-Seq Gain Traction?

2011-08-31T22:59:00.000-04:00

At the beginning of the month, I had dinner with J Adams from Azco Biotech and some friends/colleagues of his and talked over the Max-Seq. And yes, I did let them pick up the bill -- J wouldn't let me pay for myself. In Sequence did a nice piece on it the next week, so again I've blown an opportunity to scoop them. Then somehow, between vacations and other distractions, this piece was stuck in blogger limbo. But, there are some details I don't see there and some color I think worth adding.

Wishing I Had Been A Referee: A Renaissance for Tagamet?

2011-08-28T08:42:00.000-04:00

Back from vacation & watching another wave of Hurricane Irene soak the area (curiously, the windiest times so far seem to be breaks in the rain). August has not seen much attention paid to this space (indeed, I have one piece that has gestated nearly the whole month), so time to put the shoulder to the wheel.

Just before my vacation, a pair of papers showed up in Science Translational Medicine which describe two attempts at drug re-positioning by transcriptional profiling. The key concept is to take expression profiles for diseases and try to find drugs which appear to generate the opposite transcriptional pattern, with the theory that the drug could nudge the disease pattern back to a normal state. This is an idea which has been kicking around for a while, and at one time was the focus of a number of companies. One was even trying to re-position a drug I have a small connection to (MLNM developed it from a target I spotted in an EST library), but I believe that is a dead effort. One challenge in tracking this field is that it is rarely obvious what happened in the end; did a drug fail to pan out or did the backers just run out of cash?

Names in Collision

2011-08-08T22:59:00.000-04:00

I will claim that I saw this coming, in that I've toyed with the basic skeleton of this post before. But, I hadn't gotten around to it -- but how could I miss this opportunity. On a mailing list devoted to SAM, someone asked about a related topic to SAM, and one of the experts on the board replied with an electronic head-scratching

Ion Throws A Long Punch At MiSeq

2011-08-04T23:17:00.003-04:00

The benchtop sequencer wars are heating up! Illumina and Life are engaged in a fierce war of pamphlets and datasets to convince the world that they have the edge. I won't attempt to give a complete play-by-play, but hit on the latest developments, which includes Ion releasing a dataset of 250+ bp reads.
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How Many Toes Does Ion Have Left?

2011-07-29T09:21:00.000-04:00

I've previously complained about Ion Torrent's bungling and secrecy when it comes to educating their current and potential future users about key technical information. I've recently come across yet another botch, one that underscores that attempting to control information in the Internet age only serves to distract from the goal of ensuring access to correct information.