Wednesday, December 28, 2011

Year's End

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.

Friday, December 09, 2011

Reflecting on a Year of Ion Torrent

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.

Thursday, October 27, 2011

Fitting Out

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.

Tuesday, October 11, 2011

MiSeq Made Easy?

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.

Wednesday, September 28, 2011

Thinking Outside the Box or Just Plain Nuts?

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.

Tuesday, September 27, 2011

Boston's Boris Bikes

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.

Sunday, September 18, 2011


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.

Wednesday, September 14, 2011

Illumina Calls for a Flag on the Play

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!".

Thursday, September 01, 2011

Genetic Education:

   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)

Wednesday, August 31, 2011

Will Max-Seq Gain Traction?

      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.

Sunday, August 28, 2011

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

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?

Monday, August 08, 2011

Names in Collision

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

Thursday, August 04, 2011

Ion Throws A Long Punch At MiSeq

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.

Friday, July 29, 2011

How Many Toes Does Ion Have Left?

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.

Thursday, July 28, 2011

Tschuess, Shuttle!

Clearly with a week having passed since touchdown, my farewell to the space shuttle program is grossly overdue.  I actually missed watching the event live, as I was off on a camping trip in some beautiful New Hampshire woods.  
Atop of the usual excuses, it's been a bit hard to figure out what I could write that was different than so much that has been written.  It would seem that every major media outlet opined on the subject, and most did a decent job in hitting the key points. 

Tuesday, July 12, 2011

Ion's Gaggle of New Accessory Products

     Ion Torrent had a press release announcing a number of new components to the platform, as well as shipping of the 316 chip and a drop in price of the original 314 chip to $99 (alas, the announcement was not synchronized with updating the online store, so no details could be checked -- such as the price of the 316 chips).

Monday, July 11, 2011

PacBio's Foray Against the German E.coli Outbreak

    I recently remarked that it was surprising that PacBio had not jumped on the German E.coli outbreak strain, given CEO Eric Schadt's professed interest in biosurveillance.  Dr. Schadt was kind enough to spend a half hour discussing the topic with me last week, in the wake of PacBio releasing de novo assemblies of this strain and 11 other pathogenic E.coli strains (6 having never previously been sequenced) on the PacBio DevNet website. Dr. Schadt also has a detailed blog post on the project.
    In both the blog post and our conversation yesterday he explained why PacBio wasn't in the forefront of this effort but still decided to jump in. Dr. Schadt was certainly aware of the outbreak; he was in Germany at a conference when the public alarm was building. But initially, the company was trying to stay focused on the commercial launch of their instrument. However, after seeing the first public assembly come out at several thousand contigs, they consulted some academic collaborators and decided to run their own sequencing, with a goal of providing a much less fragmented assembly.  The initial thought was a hybrid assembly containing both PacBio and short read data, but after another group generated a high quality short read assembly the emphasis switched to a PacBio-only assembly.
     Sequencing proceeded rapidly, as before; about 2 days from receipt of the samples to generation of data for assembly.  Three machines were enlisted, using current generation SMRTcells but with pre-release polymerase and protocols (these are scheduled to go to customers by year's end). A number of eye-popping statistics are shown: mean mappable reads of 2.5-3Kb, 5% of the reads at 6-7Kb or greater and one herculean read of almost 23Kb!  Yield from the SMRTcells was variable, ranging from a mean per sample of 13K to 55K (overall mean of 26K).  Raw accuracy was still about 85%.
     For the German strain, both a large insert library and a small insert circular consensus library were sequenced.  One challenge that the PacBio team ran into is rapidly generating a DNA population of defined size which is bigger than about 9Kb.  The populations must have a restricted size range, or else the smaller fragments are preferentially loaded into the zero mode waveguides where the sequencing actually takes place.  Due to this, the value of the monster reads was diminished.  Indeed, Schadt sees this leading to PacBio's inability to drive their data to a single contig (the main chromosome is broken into 33 contigs); there simply weren't reads able to bridge some very large repeat elements.  This also is why they didn't use the strobe sequencing mode, which generates islands of sequence separated by statistically-defined gaps.  Given that so many of the reads were approaching the size of the inserts, strobing wouldn't do much good.
    Not very far back, I presented a somewhat bearish case for PacBio.  Do the latest results change this? As much as I love the technology and the idea of long reads, I'm still concerned that too many scientists will see these as a nice-to-have and not a must have.  Dr. Schadt mentioned they are working on projects to demonstrate PacBio sequencing of much larger (100+Mb) genomes, which is an important start.  Still, it may be that few labs will see the incremental value of long PacBio reads as not important enough, or that they simply don't need to invest in a machine but instead rent some of the existing capacity (I know of two service providers offering the system).  As PacBio pushes the reads longer and longer (imagine if 5% of the reads were 20+Kb!) it will offer advantages for closing long gaps.  For example, PacBio should require relatively little DNA for library construction, whereas some of the competing mate-pair techniques are notorious for being very inefficient at converting input DNA to usable fragments (as well as creating some level of noise from chimeras generated in ligation steps).  

Friday, June 24, 2011

MiSeq Aims for Ion Torrent

     Illumina has released a MiSeq dataset for E.coli MG1655 on its website.  Accompanying the FASTQ and BAM files is a presentation, the first half of which compares the performance to big brother HiSeq.  The second half is an explicit comparison against the available Ion Torrent. 

Tuesday, June 21, 2011

A first peek at data from an Ion 316 chip

      Ion Torrent has made available an E.coli DH10B fragment dataset for the 316 chip, which is expected to be generally available early next month.  I've theoretically had access to the data since Saturday, but a series of events (computer-free weekend, a crashed home computer, a personal day & a good but unbloggable conference) have meant that ambitious plans to analyze it are still in progress.  So, what I discuss below is either from Ion's provided information or other sources, so take it with appropriate caution.

Two administrative notes

Two administrative items:

First, sometimes comments are getting moderated very late.  I do pledge this is not an attempt on my part to bury negative commentary.  Rather, it appears that sometimes when I thought I had moderated comments via my Android phone it hasn't succeeded.   

Second, I am trying out the new smartphone-friendly layout option for Blogger.  Please let me know if you are reading this on a smartphone and hate the new layout.

Wednesday, June 15, 2011

E.coli Outbreak Genomics

     The E.coli outbreak in Germany continues to be a major news item.  It is looking increasingly doubtful that the source of the infection will be conclusively traced, as the German authorities have already named and then backed off two suspects, Spanish cucumbers and German bean sprouts.  These activities have not been without repercussions; Spanish agriculture has been hard hit and exports of European produce in general are reportedly hurting.
     On the genomics front, the outbreak has demonstrated how quickly bacterial genomics can be run on the current class of instrumentation.  BGI Europe knocked off the sequence in a series of Ion Torrent runs in 3 days, and a group at University of Muenster worked at similar speed with the Ion setup as well.  Later, sequences have come in from the Illumina and 454 platforms.  The public release of this data has engendered a number of public analysis projects.

Sunday, June 05, 2011

The Arsenic Bug, Revisited

As has been covered in many outlets, Science has released eight technical comments on the arsenic-loving bacterium issue along with a response by the authors, which I commented on when it appeared.  A good summary of the comments can be found at In The Pipeline, and has a good take on it as well.  The quick summary is that various technical and theoretical issues are presented by the critics, and the NASA team dismisses all of them by standing by their data and interpretations.  

Thursday, May 26, 2011

Paying a Painful 75% Secrecy Tax

In a post a while back, I mentioned that my Ion Torrent sequencing project was stalled because my service provider couldn't get some of the key kits, despite an Ion representative posting that no such shortages existed.  I've been remiss in updating that; last Tuesday the kits showed up and Monday I got my data -- and a bit of a shock.

Monday, May 23, 2011

MiSeq's First Light

Someone was kind enough to send me a copy of a poster by Illumina reporting results from the MiSeq.  Now, to be very upfront, by someone I mean "a person from a PR firm contracted by Illumina" and "kind enough" that she was doing her job.  I don't have illusions about motive here, the author list is all from Illumina or Epicentre, but this was a poster presented at the recent Cold Spring Harbor Biology of Genomes meeting.  It certainly isn't peer-reviewed data, but it is something. Of course, we can't know to what degree these are cherry-picked results.  If you want to be really cynical, call it messaging and not data.  Yes, I've taken some flak in the comments recently about how favorable my coverage of Ion has been, and I'm trying to adjust.  And don't worry; I have some new bones to pick in that area.

Thursday, May 19, 2011

Forums: Open Beats Closed Hands Down

Around the Internet, there are a number of communities in which scientists can swap useful information.   SEQAnswers is a very useful site I frequent; BioStar is one I don't but probably should.  Life Technologies has set up a community around Ion Torrent, and the contrast between that and SEQAnswers is a useful one.

SEQAnswers has a straightforward access policy.  Anyone can view content, but to post or reply you must register for a membership.  This approach appears to have been very successful, as there is a healthy number of individuals posting to the site.  You can browse around and figure out if the site applies, plus search engines such as Google can steer individuals in.  SEQAnswers boasts a number of authors of major second generation sequencing analysis packages, including Bowtie, Tophat, BFAST and Samtools, as regular contributors.  There is a significant network benefit to this; quality encourages quality and conversely such folks must be judicious in the number of forums they actively participate in.  The management of SEQAnswers applies a light hand, occasionally moving posts to more relevant forums and smothering all spam.  In addition to the forums, a key asset is a large wiki on second generation sequencing packages.

The Ion Community is set up on a very different basis.  It has two sections, each with its own membership restrictions.  PGM Users is open only to registered owners of the sequencing system; Torrent Dev is open to that group plus anyone registered for the Grand Challenges.  Each section has both discussion areas and documents.  The site is flashy, though more than a few links are indirect detours to what you really want.

Now, there are plenty of examples of how maintaining some control over a site can be productive.  I was recently trying to eradicate one of these nefarious fake antivirus viruses from our home computer, and on one major security software company's forums I found what looked suspiciously like a link to infect with one of these viruses.  Keeping a single point of origin for documents can be useful as well, to reduce confusion.  For example, if you Google around for information on 454 fusion amplicon design it is easy to find outdated information.  We also wouldn't want any forum to devolve to the level of the Biotech Rumor Mill, which by its very nature must allowed unregistered posters, and as a result is a mudpit of insults and near(?)-libel.

But, Ion's approach is in my opinion strongly self-defeating.  I won't go into detail here, but in the extreme form they have on two occasions (this thread and this one) argued for the suppression of information on PGM from SEQAnswers (I will try to tackle this soon, but after getting a chance to talk to at least one person with the Ion side of the story).  But it's also easy to argue from a purely practical standpoint, rather than a philosophical one, that this approach is not doing their platform any favors.

The first problem is that the closed access means that you can't lurk on the cheap there; either commit to being part of the community or stay out.  This prevents sucking people in slowly; for many the barrier of registering -- particularly since your registration does not become instantly active -- is too high a barrier.  Indeed, I would offer as evidence for this that the first major PGM-tuned software package not from Ion or a commercial partner was apparently not spurred by the Ion Community, but by Nick Loman's post on assembly of Ion data.  Nick's original post apparently received over 2K views, which must be at least an order of magnitude larger than the current Ion Community membership.

The second problem is the two layer design.  Okay, I'll admit it -- it's maddening to be excluded from the PGM Users forum.  How do I know that there are not discussions there I could either benefit from or contribute to?  If someone starts a discussion there better suited for Torrent Dev, will it get bumped up?  If so, who decides?  But, worse than that is that many technical documents that I would find valuable are beyond that access barrier.

The third problem is I find these rigid definitions completely at odds with scientific reality.  Just because I don't own a PGM doesn't mean I might try to do everything but run the instrument.  As an example on another platform, my colleagues & I have run SureSelect on Illumina where we did all the steps except shear the DNA (outsourced), prep the flowcell and run the flowcell.  Furthermore, in a modern collaborative environment, someone in one lab may own the machine but in another lab work up the samples. It's also not clear what any of this "security by obscurity" is buying; given the number of groups using Ion, whomever they're trying to hide the information from can certainly find a leak.  Ion should heed the example of the music industry, which failed to provide legitimate means to supply a growing demand for digital music, and thereby spawned widespread illegal file sharing.  Plus, many browsers are potential buyers -- people want to know what they are really buying in to and to start storyboarding what running an instrument would mean in terms of personnel and auxiliary equipment.

The fourth problem is discoverability.  How do I find information?  Well, for second generation sequencing stuff it is the trio of PubMed, Google and the SEQAnswers software wiki.  PubMed is great, but many packages show up online long before they are published.  Google is useful if you know what you are looking for, and SEQAnswers is great if someone has logged it there (and in general, once I see something I make sure it is logged there).

But with the Ion Community, those last two are problematic.  The objections Ion has raised to links going to the interior of the community mean that I don't dare put such in the Wiki; but conversely a link just pointing to the community is not terribly useful.  But worst, since Ion apparently won't let Google in their stuff is invisible to that valuable tool.  As evidence, at the moment if you Google for information on their TMAP aligner with "tmap source code ion torrent", nothing from the community comes up (but threads on SEQAnswers do!).

Ion isn't the first, and probably won't be the last, company to try to have its I proprietary control cake yet eat its Internet openness.  Life has SOLiD Community, Helicos has one for Helioscope, PacBio DevNet for SMRT sequencing and so forth.  It takes some real courage to relax some control and invite the whole world to your party.  Some folks would no doubt see view-without-registration as a loss of useful marketing data, forgetting that the openness of a site will itself draw in customers.  Anyone launching a new platform should really ask themselves, will I be better off trying to control a rare destination for a few visitors, or perhaps just cultivate a sub-community over at SEQAnswers.

Saturday, May 14, 2011

Oh Would It Be Fun to Debug Strobe Sequencing!

Through the course of a month, I easily sketch out (on average) a dozen plus experimental designs in the context of my day job.  Of course, only a very few of these are ever executed; many never get shown to another soul.  By constantly pondering how I might tackle questions, I can keep in practice and present plans which are reasonably well thought-out.  It also helps to have thought through things; sometimes a rejected plan will suddenly look like a gem due to some other result or change in priorities.
Atop that, I also sketch up a few which have nothing to do with my day job.  Partly it is fun, and partly it is a way to exercise the process on areas I can be certain of my objectivity.  A related exercise is to sketch out a business plan; I end up doing that a few times a year.  Never have taken any further than a napkin; not only do I lack the necessary thirst for risk, but most are for businesses I'd be happier being a customer than an employee.

For example, after a recent lunch with a friend from graduate school I found myself again contemplating a question that had arisen at Codon in the context of gene synthesis.  We didn't have second generation sequencing there (if Codon had survived, we certainly would have launched into it at some point) and had seen the hint of an interesting phenomenon (and practical problem) but could have never collected enough data to really nail it down.  Now, with sequencing cheap on a large scale, and this being the perfect sort of problem for such sequencing (since one would need only very short reads), it was short-term obsession to work out how to run such an experiment.  For probably $5K and a tiny bit of molecular biology, a nice little paper -- pity I don't have a slush fund to cover it.   My apologies for not supplying any details; maybe I will someday have some found money to cover the project.

However, I did just get another idea that I might as welll be open about, as for one it will probably be solved in the near future and two there is no opportunity to actually work on it.  So it can be fun to speculate in the open on how to address the problem.

Friday, May 13, 2011

Blogger glitch

Blogger experienced an outage which I found out about today.  This caused my last post to disappear; any posts or comments in a certain time period were lost.

Thanks go out to the anonymous reader who posted a comment wondering where my last post went.  Blogger (Google) did not notify me of the issue.  The really disconcerting part is the Google cached version of the post was missing as well -- this suggested something very odd going on.

I often write posts directly in Blogger, so I don't have a backup.  This was an exception & I did actually have the rough draft, which I would have posted if the old one wasn't restored.

Wednesday, May 11, 2011

Ion's Growing Pains

A recent In Sequence article indicated that Ion Torrent is enjoying strong initial sales.  This bodes well for continued evolution and improvement of the technology, as LIFE will continue to smell revenues and opportunity.  Ion has announced a number of improvements, but most aren't scheduled to arrive until the near future.
The challenge is for LIFE to keep executing on their plan.  Already some issues have arisen; my own Ion experiment at a service provider is stalled due to a back-ordered template prep reagent (two weeks and counting!). This is a key reason to do pilots on emerging technologies with non-critical (but interesting) samples; I was bitten last fall by another backorder bug (that time, the paired end SOLiD reagents).  Of course, this time it is even more complicated, as Ion is making a major change to both the underlying kits and to the software to process the data.  It will be worth it if I get results anything like Ion's provided E.coli 314 dataset, which has about 4.5X the data of the original 314 chip spec.

Sunday, May 08, 2011

Ion Torrent's Data Quality Is Pretty Good (and Better Than Ion Claims)

One of the key questions around Ion Torrent, as with all new platforms, is what is the sequence data quality like.  Now, that can be a loaded question but I'll ask a slight variant on it: how truthful (or accurate) is Ion at estimating base quality?

Quality scores are a useful adjunct to sequencing data and are commonly expressed as phred scores, which are the integer part of -10*log10 of the error probability.  Any base caller needs to estimate these and many downstream programs, from aligners to assemblers to variant callers, rely on these quality values for their operations.  In many cases, the individual quality scores are combined to generate some joint estimate of the error (I built one such model at Codon).  These error probabilities come not from an infallible source, but are rather estimated from aspects of the raw data.  

Saturday, May 07, 2011

Which numbers did I use this time?

Noted screenwriter William Goldman's second memoir on the film industry is titled "Which Lie Did I Tell?".  The title is not a quote from Goldman, but rather what another movie industry said after getting off a long phone call he had taken in Goldman's presence.  I'm a bit nervous I inadvertently strayed in that direction in my last item on Pacific Biosciences.

I was relying on memory for my numbers & in the course of writing things I think I also revised those downwards, not out of malice but rather an attempt to be conservative.  As a correspondent pointed out, the first pass accuracy on the first commercial system is claimed to be 85%, not 80% as I stated.  On the number of reads, I failed to update for the newer SMRT cells which are out; I said 10K and it's probably at least 3X that.  However, I do have a bone to pick.

Monday, May 02, 2011

Wednesday, April 13, 2011

Better Template Prep for Ion Announced

One of the perceived weak points of the Ion Torrent, in contrast to the Illumina, has been the use of emulsion PCR for template preparation.  The original template prep protocol was apparently around 10 hours of wall clock time, with a substantial amount of hands on time.  Improved template prep is the subject of one of the Grand Challenges.  A new kit being released today along with a new instrument announced today (but not generally available until late summer or sometime this fall) go after this issue; the new kit providing an inexpensive but substantial immediate improvement and the modestly priced template prep instrument providing a very low labor solution once it arrives

Tuesday, April 12, 2011

Vostok & Columbia

It has hardly gone unreported in the media that today marks the 50th anniversary of the manned spaceflight and the 30th of the first space shuttle launch.  It was an accident of scheduling delays that put that flight on the 20th anniversary of Gagarin's, but what an appropriate synchrony that is!  My own contribution herein is to pen two quick capsules of two books that deserve longer reviews: Two Sides of the Moon and Riding Rockets.  If you have a strong interest in the history of spaceflight, you should consider reading each of these if you haven't already.  The only caveat I'll throw in is that if you have a young friend who fits that category, but you do not, you should at least skim Reading Rockets before passing it on; some of the content (and most of the humor) is of a mature nature.  While neither book is primarily about either of the events commemorated today, both bear on it.

Friday, April 08, 2011

Gnoteworthy But Gnot Gnoticed

A commenter on yesterday's piece on Intelligent Biosystems scolded me on not mentioning GnuBio and said they had released data.  This had totally slipped my my notice, and indeed it seemed to have slipped past the GenomeWeb and BioIT worlds as well, judging from some Google searches.  There is certainly a press release out there and covered by several outlets, but amazingly stealthy for public relations.  Strange!  But many thanks to my anonymous correspondent for flagging me on this!

But, it does make a set of stunning claims.  When GnuBio launched last year and announced they would have alpha instruments in collaborator's hands by the end of 2010, I was skeptical.

Another Low Cost Sequencer on the Horizon?

An article in GenomeWeb's In Sequence (which, alas, requires a subscription for which I've never sprung) has a piece on Intelligent Biosystems (IBS), which iat the X-Gen Congress meeting apparently announced a plan to launch the "Pinpoint Mini" sequencer.  The box would come in at $85K, putting it smack in the middle of Ion Torrent PGM and Illumina MiSeq pricing.  The hope is to have boxes shipping to early access customers by the end of the year.

To be honest, I'm guilty of mentally writing off IBS, as they had been around a long time and very quiet.  Indeed, in my defense their website looks like it hasn't been updated since it first went up, and you'd think now that they made a big announcement it would be updated, but apparently not yet.  On the other hand, while stale websites can indicate fading companies, the fact that it still is working suggests some life.

In any case, I was apparently hasty in my thoughts.  The box as described has some interesting features.  Supposedly it will crank out data at $75/Gbase.  The claim is that one exome could be sequenced (reagent costs only, mind you) at 30X for $150 in about 1.5 days.  No word on read lengths.  The system will mount 20 flow cells, each of which can be run independently.  Chemistry is based on reversible terminators that they exclusively licensed; if I understand it correctly the big advantage of their chemistry is simplicity.  There's also a curious bit in the publication from the founders is using a mix of unlabeled reversible terminators with labeled dideoxy terminators; the same cleavage reaction removes both the terminator and the label.  This was touted as a way to reduce the discrimination of the polymerase against the reversible terminators.  Of course, an alternative would be to generate mutant polymerases which are more amenable to being fed terminators.  Having four pairs of complicated compounds wouldn't seem to be a route to low cost, but perhaps the gains are worth it (or this chemistry isn't being used any more; very hard to tell from what I was able to read).

Sounds great, but of course there's a lot to do before such a machine can launch.  There's no word about sample prep method, which probably means it will use emulsion PCR, since necessary licenses for that can apparently be obtained.  There's also the problem of manufacturing the instrument and the reagent kits.  Te fact that IBS apparently planned to launch a PinPoint large-scale sequencer a few years back and couldn't get it out the door is not going to help them compete in the expectations market with the other boxes.

One solution to some of these issues would be a strategic partnership with (or outright acquisition by) a major reagents and/or equipment player. It's not hard to come up with a list of candidates, based on nothing more than that description.  Perhaps at some point Affymetrix will decide to move into next-gen.  Roche could always decide to go for something cheaper than 454, but I doubt it.  Agilent seems quite happy supplying picks and shovels, but perhaps they'll go for the big time.  Perkin Elmer, GE (which is working on blue sky sequencers) or a host of others.  Picking the right partner will be key; Illumina has the advantage of an enormous installed base and thriving ecosystem of associated vendors, whereas Ion Torrent has a lot of buzz and serious marketing muscle (not to say Illumina is lacking there either).

It's also interesting to see this machine being touted as an exome sequencing workhorse for clinical use.  The issue really deserves its own detailed post, but such an application brings some serious issues.    Library preparation requires a lot of labor and a bunch of other instruments, or a bit less labor and some more instruments specialized for prep.   Right now, the market for exomes on HiSeq using either SureSelect or EZCap  is quite competitive; I've recently gotten quotes ranging from $2K-$5K (the lower quotes tend to be from new entrants; promised coverage varies a bit too) .  For 50Mb capture at 50X coverage, it would seem you could get around 50 exomes into one HiSeq flowcell, which at $10K each means about $200 in sequencing (feel free to correct my math in the comments).  That would suggest that very little of the cost of these exome captures is sequencing reagents; the majority is labor and the EZCap or SureSelect kits.

While some elegant library-free methods  (really, methods which add the sequencing adaptors as they are capturing the targeted DNA). for exome sequencing have been published, none of these are commercially available on an exome scale.   RainDance requires an expensive ($200K+) box and isn't quite up to exome scale,. .  Halo Genomics. has announced a library-free  prep for "1000s of exons", so perhaps this will break this problem open.  Whether this is really whole exome, or something smaller, remains to be seen.  A safe rule, though, is that these methods are only efficient if read lengths are significant.  At a minimum, the first part of a read is burned on getting through the targeting primers, and with very short reads the size of each targeted amplicon must be small, meaning for a fixed number of amplicons (cost) you can capture a lot less DNA than with a longer read technology.

So, another player in the field -- but with a far off beta release and a lack of a track record.  They'll be fun to watch (assuming they go out of possum mode), but probably won't be a real factor in the market for over a year.

Tuesday, April 05, 2011

Can we treat the kinase du jour?

For the second time in just over a week, the Boston Globe Sunday was discussing protein kinases in the context of cancer.  A group from the Broad has just published a sequencing study (Sanger!) identifying mutations in the protein kinase DDR2 in about 4% of squamous cell carcinomas of the lung.  This is a common form of smoking-induced non-small cell lung cancer (NSCLC) and one for which many therapies useful in lung cancer are contraindicated.  The prior study by another group at the Broad was published a bit over a week ago in Nature detailing an extensive look at myelomas by sequencing, and found mutations in the kinase BRAF in 4% of myelomas.

The myeloma study is quite a watershed and in some ways raises the bar for cancer genomics publications.  Whereas most papers have published a single cancer genome and a few have published single digit genomes, this one looked at 38 myelomas.  Now, not to overstate things, as only in 23 patients were matched normal and myeloma whole genomes sequenced; for the other 15 patients just the exomes were sequenced (one additional exome pair was run in a patient with whole genome sequencing, to enable comparison).  Clearly this is a serious scaling up of effort, enabled by dropping costs.  By sequencing multiple genomes, the possibility exists both to discover rare variants as well as get some rough mutation frequency information.

The myeloms study is curious in one aspect: the results were first discussed about a year ago at AACR, the big pre-clinical meeting going on right now, and were described as submitted at a conference I attended at MIT last June.  Indeed, the paper states "Received 11 June 2010; accepted 17 January 2011".  While there is a bit of functional investigation of one gene (siRNA vs. HOXA9) and some Western blots of coagulation factors, this is primarily a genomics paper.  Is Nature becoming reluctant to publish such papers?  What really held this up for so long?

In any case, the primary finding in both of these papers is low but measurable frequency mutation of protein kinases in human cancers.  This should come as no surprise, as a previous paper from the same groups in lung adenocarcinoma (the other major class of NSCLC), multiple kinases were found to be mutated beyond the relatively high frequency EGFR, again including BRAF but also a host of other kinases.  The new DDR2 paper also found mutations in multiple kinases, though any follow-up was focused on DDR2.  Another 5%-or-so slice of adenocarcinoma carries a fusion protein of the kinase ALK, which can be treated with inhibitors developed against ALK.  It also may be an opportunity to target ALK by a different strategy, one which my company has explored (yes, I have a financial interest there!).. The challenge is to determine which, if any, of these mutations are driving tumors and which are just passengers.

In the case of the DDR2 paper, the authors built a pretty nice story.  One big bonus to protein kinases is that there has been extensive efforts in the last 30 or so years to study them, with many inhibitors available.  A raging argument in the field is whether clinically useful inhibitors need to be exquisitely specific or can be as subtle as a wrecking ball, and the truth is that clinically approved kinase inhibitors run the gamut.  Imatinib (Gleevec)  is quite specific, though it still hits multiple kinases and that has proven useful as it has enabled targeting multiple cancers.  For example, some gastrointestinal stromal tumors are driven by c-KIT mutations and others by PDGFR mutations, but luckily imatinib hits both.  Other inhibitors such as sorafenib and suntinib  are less discriminating, but still tolerable.

In the case of DDR2, the approved inhibitor dasatinib turns out to be effective, and the new paper shows this first in cell lines.  Cell lines carrying DDR2 mutations are more sensitive to dasatinib than those which do not, but the trend continues both in mouse xenograft models and finally in a single human patient carrying a DDR2 mutation in her tumor.  Alas, the patient apparently had to discontinue therapy due to side effects.

Now that genomics has demonstrated the ability to find these low frequency mutations, the question is quite open as to how to move them into clinical practice.  One model would be to simply sequence extensively and treat each patient by the best guess for their mutations; this approach has been published and is apparently being used in the case of author Christopher Hitchens.  While whole genome or exome sequencing might be too costly or slow for routine use, targeted mutation panels are another possible approach (though honestly, exome sequencing is getting down in the $2.5K range these days).  Such targeted panels can attempt to focus on the most frequent and actionable mutations, though DDR2 in squamous cell carcinoma appears to not have any one mutation particularly favored.

The alternative is to try to run clinical trials to carefully appraise the clinical utility of these approaches.  When I mentioned the BRAF in myeloma story a while back to a co-worker (who happens to have developed multiple drugs, including an effective one in myeloma) and expressed the opinion that it is a slam-dunk to use a BRAF inhibitor (which is near approval in melanoma) in such cases, he took a more cautious view.  How do you know these are really the important mutations?  How will you know how long the treatment lasts?  Perhaps the BRAF mutations in myeloma help the tumor but are not critical.  How will you know the correct dose schedule?  Combination therapy?  Whether drug is getting to a very different tumor?  To truly answer these questions rigorously, trials are needed.

But the difficulty in running such trials cannot be underestimated.  For example, a company thinking of running a clinical trial looking at BRAF in squamous cell carcinoma faces quite a task.  Now, the market is not small: according to Wikipedia (an easy lookup late at night, though perhaps with large error bars) there are about 500K new cases yearly, and a quarter of those are squamous.  Presumably at least a quarter of those cases are in the U.S., so around 70K new cases per year.  Four percent of 70K (error bars growing with each estimate) is 2.8K patients, which is possibly attractive but getting small..

However, to get the trial going you are going to need to screen to find that 4% of patients.  Squamous is a standard diagnosis, so you can start there, but will still need to recruit, consent and screen to get that small fraction.  In the mean time, you are competing with every other trial out there to recruit, consent and screen patients.  Sure, once they miss another trial they might come to yours -- or might not.  To top it off, a lot of patients either are never offered or will never consent to a trial; the farther you are from a large academic cancer center, the less likely you will have a trial available to you.

Now, if oncogenic mutation screening becomes a standard part of cancer care, as it has at MGH and probably some other leading institutions, then if these mutations are in the panels it may be that many patients will know their mutation status before you recruit them into your trial.  But until this becomes widespread, and only if your gene of interest is sufficiently covered, will this method work.

Yet another approach is to design trials which test multiple therapies.  One prominent example in lung cancer is the BATTLE trial, which is trying 4 different therapies with an adaptive design which uses molecular testing as part of the therapy-assignment scheme.   Designs such as BATTLE are quite complicated (well beyond my expertise to critique) and get only more so with more drug regimens; if lung cancer is driven by a dozen or so kinases suggesting a slightly smaller number of therapies, can a trial to test these therapies be designed, patients accrued and useful results out?  In such studies, will they be judged by whether the study overall improves survival, or can each treatment be viewed as a separate study?  

For the sake of patients, these issues need to be tackled.  They'll be hard in lung cancer, and far worse in a disease like myeloma.  If we ballpark myeloma at 15K new cases per year in the U.S., 4% of that is getting to be a small group (600 patients).  Any sizable trial is going to need to recruit a huge fraction of these patients.  Now, with patient advocacy groups and publicity it may be possible to find that small population, but it will certainly be challenging.  Indeed, the Multiple Myeloma Research Foundation (which sponsored the sequencing) is already talking about how to support such efforts.

So, in closing, these sequencing studies are suggesting very real therapeutic options for patients.  However, driving these findings to routine clinical use, even when drugs are available off-the-shelf for the kinases of interest, will continue to challenge all of the scientists working on translational oncology research.

Wednesday, March 23, 2011

What might a PGM2 look like?

The New England chapter of the Laboratory Robot Interest Group (NE-LRIG) had a nice meeting tonight over at Astra Zeneca's beautiful Waltham campus (woodsy borders, with a view of the nearby reservoir).  The meeting was sponsored by Ion Torrent & they gave one of the three talks.  All three talks were quite good, with my friend & former Millennium colleague Sunita Badola from Amgen leading off with 454 amplicon sequencing in oncology clinical trials, followed by Mark DePristo from the Broad Institute talking about the 1K genomes effort and finally Jason Affourtit from Ion Torrent (he oversees all their field applications scientists) about the Ion platform.  The Ion talk gave a bit of the standard overview, followed by some slides summarizing the talks at Marco Island.

Now, when I've run previous items on Ion Torrent they have garnered a lot of comments.  Some of these are positive, others (and some of my posts) not so much, with some of the commenters most charitably described as downright cynical.  I won't have any data of my own for at least a month (and a machine on my own is still no more than a great desire), but I must say that if Ion Torrent is all smoke and mirrors, as some comments have insinuated, they have an awful lot of good people in on the ruse.  A friend of mine who is a very experienced genomics lab head was raving about her new machine and I happened to talk to another site today and their first four runs have all come in with greater than 2X the number of reads in the specification and very good quality.  About the only thing I've heard that is less than raving is that the quality drops near the end of the reads in a way that the effective read length is sometimes more like 80-90 rather than 100.  Still, if you know this going in you can adapt to it.

A star before and after the talks was a PGM which was available for viewing, along with 314 and 316 chips being passed around (which I was sorely tempted to have disappear into my shirt pocket, but morals prevailed).  These, for example, brought home the fact which I hadn't appreciated before that the 316 has significantly more actual surface area than the 314 chip, though it fits in the same carrier.  The difference between the chips is quite visible in your hand.  The 316 would appear to essentially max out the form factor, so the 318 can't keep up this trend. [corrected 3/25 per Rick's catching the typo]

Something that was emphasized tonight that I hadn't appreciated before is that there are no pumps in the PGM.  Reagents are propelled by argon gas pressure, managed by valves which are themselves actuated by the argon (some electrical widgets ultimately control the valves).  Also, the case apparently encompasses a lot of empty space (the Ion folks were open about this, though the machine was not open to view the innards).  Presumably some of this was a conservative design leaving space for late additions (or perhaps the server), but some had to do with wanting a visually striking design.

Since the PGM instrument itself has little to do with performance of the instrument, there isn't a need to redesign it to address sequencing performance.  However, there might be other reasons.  While it is a relatively small benchtop instrument, space is often at a premium.  A group of us from Infinity visited an academic site nearby today, and their lab made ours look spacious -- every square inch of bench was crammed with machines.  
Furthermore, seeing the machine in person made it clear that in placing it, a lab must leave some space on the right side to access the wash and waste bottles along that side.  Hence, if you really wanted to cram a lab the effective footprint of the instrument is a bit larger.
So, to engage in rank speculation utterly uninformed by any hard facts, I might imagine that a focus for a PGM2 would be an even smaller footprint.  The four tubes in the front, which hold the nucleotides for sequencing, could be rearranged in a manner still artful (perhaps a diamond?) yet far more compact, enabling the side bottles to move to the front.  Perhaps the screen could move down below the instrument -- or become an off-machine accessory capable of driving multiple instruments.  Alternatively, perhaps the screen would be mounted behind the flowcell access hatch.  This hatch on top (dark grey) for placing the flowcell also seems larger than necessary.  So, if you really could combine all these, it could yield an instrument with an effective footprint about one half as wide or maybe better.

A question I didn't think to ask tonight is how sensitive is the instrument to the flowcell being level.  I'm guessing (but certainly not a confident guess) that such devices mostly don't care; at these scales gravity isn't a dominant force.  In that case, the hatch might be turned to open outwards, enabling a redesign to improve the ability to stack the instruments vertically.

Another obvious dimension would be a multi-flowcell instrument ala HiSeq 2000.  Could most of the mechanical simplicity of the system be retained while enabling multiple flowcells to be run in parallel?  That would be the key question.

Of course, the key driver for many of these would be if groups wanted multiple machines to drive very high throughput.  I think there will be a market for this, but it is premature to think it has developed.  And, it will be critical for such operations to have the promised emulsion PCR improvements (or replacement) which is promised.

Tuesday, March 22, 2011

What's On Your Cheat Sheet?

After years of scribbling on a motley collection of pads, during my time at Infinity I've been nearly rigorous about using a single notebook for my notes -- seminar notes, phone numbers, to do reminders, random thoughts (even blog ideas).  The book itself is a cheap permanently bound notebook from the local drugstore; I think they are less than $1 each.
The inside back cover of my notebook is titled "Useful Information", but I don't find very much there.  Mostly it is a lot of conversion factors, but primarily for Imperial units that nobody every uses: gills, hogsheads, penny-weights, rods, scruples and such.  Also such routinely accessed information such as the weight of a bushel of potatoes (60 pounds) or 1 barrel of flour (196 pounds) Other information include a 12x12 multiplication table, which was drilled into me over 30 years ago.  For the metric system, about a third of the page is taken up giving the same series of prefixes with each unit.  Another section has some Imperial to metric conversions.
It's interesting to think about what is curiously absent from the page.  For example, the common measurements for kitchen work, tablespoons and teaspoons, are absent.  Nowhere does a carat appear, nor conversion factors for the three different kinds of ounces (avoirdupois, troy and apothecary, for any European readers blissfully unaware of Imperial units).  I've also missed a "stone", which is a unit of weight that shows up in historical novels -- perhaps it doesn't have precise definition.  The weight of water is given in terms of a cubic ft being 2.48 gallons and weighing 62.425 pounds, rather than the usual "a pint's a pound the world around".
There are two odd values on that page given all this, but that's because I wrote them there.  It is a handy place to stash info, so I have written down that 1 human genome = 6 pg of DNA (checking that in Wikipedia, apparently it is really closer to 7: 6.95 & 6.8 for female and male respectively) .  The other odd value is 1 bp = 660 daltons.
Now, if I'm going to scribble in a few, why not add a bunch?  Indeed, while Google will happily tell me there are 8 furlongs in a mile, it won't directly answer how much a human genome weighs.  Nor will WolframAlpha -- it gave me information on human body weight in pounds.  So, what else could I need there -- and if I were printing up a bunch what would I put there.
Some of the more useful molecular biology reagent catalogs have whole sections of such information.  That is one challenge in designing such a information table; to be really useful it must be packed with information but at a density allowing high readability.  Plus, while the catalogs use many pages, I'm trying to cram it into 1 or maybe a few (the inside cover has an equally useless class schedule grid, useless to me that is).  Should I only put in what I truly can't remember, or also the things I don't have nailed so well that I can reproduce them quickly and confidently?
So, here are my current candidates, some for me and some if I were going to try to make a generally useful one.  Of course, a lot of what is valuable for ready reference depends on what you are doing.  At Codon I had a sheet taped by my desk with the sites for the restriction enzymes I used the most.  If you have a favorite vector, the polylinker map is a useful reference.  On the other hand, Planck's constant is a really important number, but one I've never needed to use in biology.  So I wouldn't bother using space on it.

  • IUPAC ambiguity codes for nucleotides.  Most I know by heart (or figure out quickly; the codes for 3 nucleotides are near the one letter they leave out), but M & K have always been a challenge.  As part of cramming for this post, I now have a mneumonic that works for me: M is Methyl, for A and C, which are capable of being methylated (I think the mnemonic is supposed to be on the native structure, but I don't know that well enough).  K is now the other two.
  • Amino acid single letter codes.  I don't need this, but for a mass produced one it would make sense.
  • The genetic code -- without trying, I have actually memorized this, but I'm not very fast working purely from memory nor am I always confident (which is why I'm not fast)
  • SI prefixes in order.  Again, I know most of these until you get to the two extremes, but usually have to rattle them off in order (milli=-3, micro=-6, nano=-9, pico=-12, etc).  
  • Powers of 2.  For up to 2^12, I can rattle these out.  Higher sometimes comes in handy.
  • Tm calculation estimation using G+C and A+T counts.  I don't use this often & don't really trust it, but for ballparking a Tm it might be worth having around
  • 1 mm^3 = 1 uL and 1000 um^3=1 pL.  Useful little conversions I found when I was exploring emPCR stuff (should I also put the formula for volume of a sphere in there, since I initially wrote it out incorrectly in that post?)
.That doesn't seem like nearly enough to fill up the page, but perhaps that's a good thing.  I probably don't know what else it would be useful to have there, so blank space to scribble more isn't a bad idea.

Friday, March 18, 2011

My Noisy Neighbors

My neighbors are up to their loud antics again; a really wild singles party. Fact of the matter is, I checked very carefully one evening before we bght the place to make sure the sound levels were what I was looking for.

Luckily, I'm not talking about a frat house or a heavy metal bar. A neighboring property has a vernal pool (a body of water which dries out in early summer, and hence cannot support fish) and the spring peepers (aka chorus frogs) tuned up for the first time of the season. Along with visiting a sugar house to see (and smell!) maple sugar being made, it's my favorite part of spring in New England.

Tuesday, March 08, 2011

What will be the last Sanger genome?

Even when I was finishing up as a graduate student, and only a few bacterial genomes had been published, one would periodically hear open speculation as to when the top journals would quit accepting genome sequencing papers. The thought was that once the novelty wore off, a genome would need to be increasingly difficult or have some very odd biology to keep getting in Science or Nature or such.

Happily, that still hasn't happened and genome sequencing papers still show up in the whole range of journals. I don't claim I scan every one, but I do try to poke around in a lot of the eukaryotic papers (I long since gave up on bacterial; happily they have become essentially uncountable). Two recent genomes in major journals, Daphnia (water flea) in Science and Pongo (orangutan, not dalmatian!) in Nature show that the limit has not yet been reached. These papers share another thread: both genomes were sequenced using fluorescent capillary Sanger sequencing.

Sanger, of course, was the backbone of genome projects until only very recently. Even in the last few years, only a few large genomes have been initially published using second generation technologies

Wednesday, March 02, 2011

Emulsion PCR: First Notes

One theme in some of the comments on my Ion Torrent commentary has been around the limitations of emulsion PCR. Some have made rather bold (and negative) predictions, such as Ion Torrent dooming themselves to short read lengths or users being unable to process many samples in parallel without cross-contamination.

Reading these really drove home to me that I didn't understand emulsion PCR. I've done regular PCR (once in a hotel ballroom, of all places!) but not emulsions. It seems simple in theory, but what goes on in practice? My main reasoning was based on the fact that emPCR is the prep method for both 454 and SOLiD; 454 clearly demonstrates the ability to execute long reads (occasionally hitting nearly a kilobase) and SOLiD the ability to generate enormous numbers of beads through emPCR. I also have a passing familiarity with RainDance's technology (we participated in the RainDance & Expression Analysis Cancer Grant program). But, I've also seen a 454 experiment go awry in a manner which was blamed on emPCR -- a small fraction of primer dimers in our input material became a painful fraction of the sequencing reads. Plus, there is that temptation to enter the Life Tech grand challenge on sample prep, or attempt to goad some friends into entering. So it is really past time to get more serious about understanding the technology.

So, off to the electronic library. Maddeningly, many of the authors in the field tend to publish in journals that I have less than facile access to, but between library visits, PubMed Central and those that are in more accessible journals, I've found a decent start.

Tuesday, March 01, 2011

When Will Life Technologies Get Serious About Their Grand Challenges?

My recent run of posts on Ion Torrent certainly garnered a lot of comments, and it would be much less than honest to say that many of the comments were far less favorable to Ion Torrent than what I have written. Indeed, many were not terribly favorable on me given what I had written about Ion Torrent -- one even asked if I "felt used" as part of a publicity stunt. (BTW, I don't -- if I can't ask the hard questions I have nobody to blame but myself).

One Ion's other very public events around the Ion Torrent has been to announce a series of three challenges to improve the performance of the instrument system (a fourth has been announced centered around SOLiD and three others have yet to be unveiled). The winner of a challenge can get $1M in prize money.

Now, contests along these lines have been successfully used by companies and organizations to drive technologies forwards. Netflix successfully crowdsourced better prediction of a user's movie tastes. The most spectacular success for such a contest was the winning entry for the Ansari X-Prize, SpaceShip One. Google is currently sponsoring a contest to land a rover on the moon and transmit HDTV images, which I look forward to eagerly.

Unfortunately, so far Life Technologies & Ion Torrent's contest seems to be all hat and no cattle. While the three goals have been announced (double the output per run, halve the sample prep time and double the accuracy), nothing else is in place. Each competition is apparently separate; there's no prize for halfway success on two of the axes. If they are serious about attracting competitors, they need to get down to brass tacks.

Now, I can't say I'm surprised. Not only has Ion shown a penchant for loudly trumpeting their progress prior to demonstrating it, but in their previous contest showed a certain degree of haste and a few punchlist items. In the first contest, submissions for how to use the instrument were judged to yield two U.S. winners (followed recently by two European winners). Each submission consisted of two parts; in the original rules it wasn't clearly stated what the distinction was between the two parts (perhaps it should have been obvious, but I don't routinely write grants) other than the rules stated a word limit for one of them. Once you tried to submit, however, then the word limit on the second section became apparent. Ion also ended up extending the deadline for submissions, which can either be seen as generous or irritating -- in the latter case, if you've burned midnight oil & spent part of a vacation chopping down an overlong second section to get your entry in on time. Importantly, that contest has a tiny fraction of complexity of any one of these contests.

Starting with, what are the rules? One key question will be around cost. For example, can a winning entry for sample prep use an instrument that costs much more than the PGM? That's not an absurd concept. Can the double the output prize be won by a sample prep process that takes a long time? For example, can I assay to find only DNA-bearing beads & then use a micromanipulator to position them? That is obviously a deliberately absurd proposal. But, unless the rules are carefully crafted someone will attempt a silly entry, and Ion will have a real mess if they are forced to put the laurels on silly.

A key & challenging area is around intellectual property (IP). The first obvious issue in this department is how much IP can you retain when submitting an entry? Obviously Ion isn't interested in paying out $1M to something they can't use -- so is the $1M in effect a license fee (with no royalties?)? On the other side of the IP coin, how much IP can a winning submission use which the submitter does not have rights to? For example, some wag might submit a sample prep protocol that is bridge PCR using in part Illumina reagents. But more complicated would be methods that only an IP lawyer can decide either infringe or build on some prior patent. If it's Life's patent, presumably they wouldn't care -- but an Illumina or Affy patent would be an entirely different fish.

Materials are going to be another critical issue issue for the yield and sample prep challenges. Any reasonable scheme for attacking these is going to get very expensive if complete kits must be purchased each time. For example, you may want to hammer on the beads without ever actually putting them on a chip. Will Ion give at-cost access to the specialized reagents (such as beads)? Furthermore, how much information are they willing to give out on the precise specs. For example, suppose a concept requires attaching something different to the beads than standard -- will specifications be provided to create appropriate beads?

Another key question is what samples? Will Life Tech supply the samples to use for improving yield or does a group get to define them? A devious approach to winning the prize would be to develop a sample which preps very badly with the standard prep. An attempt could be made to legislate this possibility away, but there would be significant advantage to standardized samples. But should these be real world samples, idealized samples (such as a pure population of a single fragment) or deliberately hard real world situations (e.g. an amplicon sample with a high fraction of primer dimers)? In a similar vein, what dataset will be made available for the accuracy challenge?

Now, Life is promising more information this Spring, and since that is still a few weeks away (or do they go by Punxsutawney Phil?). I really hope in the future they try to hold back their announcements until they're really ready to go. It doesn't help that the Twitter rehash scrolling on their screen is full of links that might provide more information, but none of them work. They really need to rethink their strategy of piecemeal delivery that can do nothing but frustrate the possible entrants in the contest.

Part of my frustration is I can't help but ponder throwing my hat in the ring. It's not hard to think of ideas for the sample prep problem and while I couldn't do the experiments I do have friends who could (time to get the core Codon team back in action!). Of coures, working out the IP headache would be an issue (unless the work was done at work, which is sadly too far afield of what we do to be a responsible course). I can also imagine a number of academic groups and even a few companies which might seriously consider entering some of these challenges. I'd love to talk up the accuracy challenge with computer geeks I know. The problems are of a very attractive sort for me -- you can very quickly generate very large and rich datasets, enabling quantitative approaches (such as Design of Experiments) to optimization. A lot of data can be generated without actually running chips but using even lower cost methods (such as microscopy or flow cytometry) to measure key aspects. But with nothing concrete to point at, it seems rather pointless to start scheming.

But, while I can't actually move forward on any of these, I can do a bit of homework on emulsion PCR. I'll try to write up that homework later this week, as it's been informative to me and I believe puts me in a better position to handicap Ion Torrent's claims on sample prep -- and various comments on emPCR from the previous posts.

Thursday, February 24, 2011

Reflecting & Responding on Today's Comments

It's nice to see my piece on the Ion Torrent 318 chip get a lot of comments, as well as being tweeted and some additional comments at SEQAnswers. I love getting comments, especially those that constructively challenge my analysis.

Two commenters threw some cold water on my enthusiasm, pointing out that the 318 is not scheduled to be released until September, and then only to early access customers. I'll confess to not asking careful enough questions on the timing & letting my desires get ahead of me. Ion Torrent will need to deliver these chips on time and working at specifications in order for scientists to believe that there really will be the promised regular upgrades. MiSeq is vaporware at the moment also, but Illumina has a strong track record for rolling out instruments.

One commenter took me to task for suggesting that Ion Torrent will simply roll right over Illumina. I don't mean to suggest this will happen, only that Ion Torrent may offer a very stiff challenge. If the PGM chip upgrades, sample prep improvements and read length improvements come as promised, then the PGM may well march up through Illumina's product line. That's not to say Illumina will remain static; they have clearly demonstrated great skill at pushing their platform to amazing abilities. The MiSeq may offer a new path to greater performance; there has already been speculation over at SEQAnswers on possible paths forward. For example, will the faster cycle times mean an opportunity for longer read lengths (if the reagents are not stable over very long runs)? Will Illumina roll out a multi-flowcell version of the MiSeq, enabling very high-throughput rapid-turnaround sequencing? I'd put more money on the latter than the former. Another thread has surfaced rumors that a HiScan upgrade is imminent which will give it HiSeq-like capabilities; for groups running both arrays and sequencing this could be useful. How much denser can Illumina pack the flowcells? Only time will tell. But, as I pointed out before, longer reads will have limited impact on overall throughput if the two reads are overlapping (though accuracy may be improved).

On the other hand, I do see as excessive cynicism (bordering on editing the truth) that AGBT had only Ion Torrent talking about Ion Torrent; given that two talks (Bolen from NCI and Nusbaum from the Broad; the Bolen talk will apparently be at ABRF as well) described actual experiences. Granted, neither was really independent of the company. It is critical for Ion Torrent's reputation that data start appearing in public spaces, especially data from regular customers.

Ditto for the experimental protocols; one commenter had a question about amplicon sequencing which will be important for Ion Torrent's success. The sooner applications are adapted to the system, the sooner customers will be buying machines and chips. Of course, a great strategy IMHO would be to put some sequencers in the hands of genomics bloggers.

As far as the question of reads per chip increasing faster than the number of sensors per chip, my understanding is that Ion Torrent expects that better sensor loading and utilization. Again, how vaporous is this? That's hard to tell -- and why feedback from actual users is desperately needed.

On the question of amplicon and read length for Ion Torrent, those would seem to be different fish (though I don't have direct experience). Amplicon length will be a matter of the emPCR conditions. I'm unaware of any signal amplification in the 454 chemistry -- I thought the signal cascade was strictly linear. But, again that is outside my expertise and I would enjoy being educated on the subject.

With regard to whether emPCR can be converted from a liability to a non-issue, it's reasonable to be skeptical. But, it isn't obvious why emPCR can't be compressed in time (though I haven't done emPCR, so that's a stretch for me to comment on). In my discussion with them, they pointed to cutting the number of cycles as one time savings. In any case, how hard as anyone tried to really optimize emPCR for speed? Only on the 454 might it have been a serious concern, and the cost of a 454 run is not going to encourage many folks to push for many runs a day. On the other hand, I don't see it as "disingenuous" the comparison I made; I've been at a company that had techs running PCR (again, conventional not emPCR) day in and day out, and any company that runs production Sanger is in a similar boat. Indeed, any big SOLiD or 454 shop must do this as well. What will the nature of the new emPCR kit be? I have some speculations, but that's a whole 'nother post.

One other surprise today from Ion Torrent is the announcement that they have sequenced the genome of Intel co-founder Gordon Moore. One claim from this is that the coverage was more uniform than with other platforms. Obviously, either publication or release of the data is needed to vet this claim. Even if they used 318 chips, this was an expensive demonstration project (I don't know the actual coverage; I don't have a subscription to In Sequence) -- even at 10X coverage it would be $20K (retail) in chips. Apparently this was an exclusive for GenomeWeb's In Sequence, as Ion doesn't even seem to have a press release out. I hope they plan to publish this in a journal soon, or if not make the primary data available for further study.

Wednesday, February 23, 2011

Has Ion Torrent Taken A 318-Sized Lead over MiSeq?

About a week ago, Ion Torrent's President Greg Fergus and Head of Marketing Manesh Jain were kind enough to engage me in a nearly an hour of discussion about the Ion Torrent platform. One agreement prior to our discussion is that I would withhold this piece until their announcement today of the 318 chip for the system (I also volunteered to let them see a draft of this in advance to ensure I had not misrepresented anything).

A key theme on their side is a certain degree of feeling that the wrong questions are being asked in the analysis of PGM versus MiSeq -- and an eagerness to shift the discussion. They wished to emphasize a number of points, and after the discussion I can see the validity of many of these.

Is Being Lucky the Same as Being Smart?

Forbes has an article co-written by Matthew Herper and Robert Langreth titled "The Next Big Move For The Smartest Biotech Investor", profiling Randal Kirk. Kirk is described as one of the few billionaires who can ascribe that status to biotechnology. Kirk made his money through two companies in the psychiatric drug space: New River Pharmaceuticals developed an ADHD drug (lisdexamfetamine) and then was acquired by Shire whereas Clinical Data developed an antidepressant (vilazodone) and was then purchased by Forest. A key part of the article profiles Kirk's investment in a little-known and secretive synthetic biology company called "Intrexon".

The title is probably meant to gall; it certainly raises my hackles. The most obvious quibble is that it isn't clear either of the drug development companies were really biotech. Of course, that would require defining biotech, but it ideally it would refer to companies which highly depend on recombinant DNA and related technologies. Now, such technologies are embedded in virtually all drug development today, but neither of these drugs sounds like they used much. Both drugs are interesting twists on prior approaches (though I'm not enough of a chemist to judge the novelty of vilazodone).

Sunday, February 20, 2011

Will Cheap Gene Synthesis Squelch Cheaper Gene Synthesis?

Among the vast piles of items which I've meant to write about but have slipped are a paper last year on gene synthesis and some subsequent announcements about trying to commercialize the method described in that paper. This is an area in which I have past experience, though I would never claim this gives me indisputable authority or omniscience in the matter.

The paper, primarily by scientists from Febit but also with two scientists from Stanford and George Church in the author list, finally describes an interesting approach to dealing with some serious challenges in gene synthesis which substantially increase the costs. By finally, I mean that the idea has certainly been kicking around for a while and was mentioned when I visited Codon Devices in the fall of 2006 looking for employment.

To fill in some background first, gene synthesis is a powerful way to generate DNA constructs which can enable all sorts of experiments. The challenge is that the cost of gene synthesis, currently starting at around $0.40 per base pair for very easy and short stuff (say, less than 2Kb), tends to restrict what you can use it for. I have a project concept right now that would be a slam dunk for gene synthesis -- but not at $0.40/bp (which I think I couldn't even get for the project). Whack that price by a few factors of two and the project becomes reasonable.

There are many cost components to commercial gene synthesis, and only someone who has carefully looked over the books while wearing a green eyeshade is going to have a proper handle on them. But three of the big expenses are the oligos themselves, the sequencing of constructs to find the correct ones and labor. What the Febit paper does is illustrate a nice way to tackle the first two in a manner that shouldn't require a lot of labor.

The oligo cost is a serious issue. Conventional oligos can be had for around $0.08 or maybe a bit less a base. However, each base in the final construct requires close to 2 bases in the oligo set. Some design strategies might get this down a bit. However, conventional columns generate far more oligo than you actually need. An approach which has been published (but not commercialized as far as I know), is to scale down the synthesis using microfluidics. This method matches better the amount synthesized and the amount you need, though the length and quality of the oligos needs refinements from what was reported in order to be truly useful. Microarrays are a means to synthesize huge numbers of oligos, but their quality also tends to be low and the quantity of each oligo species is much too small without further amplification. Amplification schemes have been worked out, but add to the processing costs of the oligos.

What Febit and company have done is take those microarray-build oligos and screen them using 454 sequencing. The beads containing the amplicons with correct oligos are then plucked out of the 454 flowcell (with 90% success of getting the right bead) and used as starting points.

Now, this has several interesting angles. First, it has been challenging to marry the non-Sanger new sequencing technologies to gene synthesis. The new technologies tend to have short reads, too short to read even a short construct. The new technologies also require library construction and it is difficult to trace a given sequence back to a specific input DNA. In other words, short read technologies are great at reading populations, but not individual wells in a gene synthesis output. Sanger on the other hand, is ill-suited for populations but great for individual clones. One solution to this problem is clever pooling and barcoding strategies, but these necessitate having enough different clones to be worth pooling and barcoding. In other words, second generation sequencing is difficult to adapt to retail gene synthesis, but looks practical for wholesale gene synthesis.

Getting the oligos right has important positive side-effects. While the stitching together of oligos into larger fragments (and larger fragments into still larger ones) can generate errors, and awful lot of the problems stem from bad input oligos. Not only can error rates be troublesome, but some of the erroneous sequences may have advantages over the correct ones in later steps. For example, a deleted fragment may PCR more efficiently than the full length, and slightly toxic gene products may be disfavored in cloning steps over frameshifted versions of the same reading frame. So, by putting the sequencing up front it should be possible to reduce the later sequencing downstream. So even if that sequencing remains Sanger, it should be possible to do a lot less.

Okay, that's the science. Now some worries about the business. Febit announced in January they are looking for investors to fire off a new company to commercialize this approach. This makes good business sense, since Febit itself must be encrusted with all sorts of business barnacles, having lurched from one business to another in trying to commercialize their microfluidic microarray system. Previously failed attempts include gene synthesis as well as microarray expression analysis and hybridization capture (I even ran one experiment with their system, whose results certainly didn't argue for them staying in that business!). The press release stated they were hoping to attain pricing in the 0.08$ per base range, which would make my current experiment concept feasible. That would be great.

Now, they will need to refine their system and perhaps adapt other sequencers. A 454 Jr would probably not be a difficult adaptation, but moving on to Ion Torrent must be tempting. Getting things to work for one paper and one set of genes is unfortunately different than being able to keep things working over an entire spectrum of customer designs.

Which leads me to where I think they will have a great challenge, though one which I think can be finessed with the proper business approach. They will be brining to market a methodology whose benefit is cost at the expense but with the caveat of attaining that cost advantage only with sufficient volume. Initially, they will be unable to reliably predict delivery times (due to kinks showing up). Finally, they are adding some additional processing steps (454 sequencing, bead recovery & oligo recovery from the bead) which may add to the time.

The abyss into which this new company must plunge is a world in which very fast gene synthesis is available from a large number of vendors in the $0.40 price range. So, they must find very large customers who are willing to be a bit patient and keep their pipeline filled. Such customers do exist, but they aren't always easy to find and pry away from their existing suppliers. In theory much cheaper synthesis would unleash new orders for projects (such as mine) which are too costly at current prices, but that is always a risky assumption to bank a company on (c.f. Codon Devices' gene synthesis business).

It's the alternative route that I predict this NewCo is likely to go down. That would be to link up with an established provider in the field. Said provider, through their salespersons and sales software, could offer each customer an option -- I can build your genes for $0.40 if you want them fast or hack that down to $0.10 a base if you can wait. In order to preserve customer satisfaction, that long time would need to include an insurance period to build the genes by the conventional route if the new route fails -- but of course if you are frequently forced to build $0.40/bp genes for which you charged $0.10/bp, that would be financial suicide.

So, in summary, I think this is a clever idea which needs to be pushed forward. But, after a long gestation in the lab, it faces a very rocky future in the production world. I hope they succeed, because it is not hard to imagine projects I would like to do which would be enabled by such a capability.

Thursday, February 17, 2011

Roads That Really Need Taking

There is a provocative Perspective piece in a recent Nature titled "Too many roads not taken". In it, the authors summarize some more extensive work (posted on Arxiv) and others showing that in several major fields of protein research, the biological community seems to be stuck on a few old favorites, with insufficient attention to other key players.

In the Nature piece, the focus is on protein kinases and nuclear hormone receptors, both key druggable classes. In the kinase area, they have a graph (the Arxiv site leads to the actual data) showing that the graph of attention (measured in bibliographic citations) given to kinases prior to 2003 is generally predictive of the attention given them in 2009; only a handful of kinases with little attention in the first time period are hot areas now. Of course, if the rest of the kinome were boring this would be justifiable, but they point to several papers which indicate that many of the unstudied kinases (for example, this series of shRNA experiments)

A very striking conclusion is underlined by their plot of NHR citations by gene, which is expanded upon significantly in the Arxiv preprint. Their contention is that the availability of chemical probes drives analysis in this family, and in their rank-ordered histogram of activity the proteins with chemical ligands are all at the top of the list. Granted, at the breakpoint the bars are nearly equally tiny on either side of the divide, but it does suggest a strong correlation. Easy to build universal approaches such as RNAi are very powerful, but especially for any kind of in vivo study are suboptimal -- not only are they hard to deliver, but utterly wiping out a protein is not a subtle way to probe a system. The Arxiv piece goes into more detail and posits that you really need good compounds, ones with good bioavailability and such. In other words, drug-like compounds.

So, they plead that we need to invest more in getting such compounds into the research community. Some of this could take the form of funding screening efforts in the public sphere, which like sequencing the human genome isn't the sexiest project from a scientific perspective -- just like the foundation is never the sexiest part of a great building. But foundations matter!

An alternative, suggested by the Arxiv paper, is that compounds may exist in the patent literature but are not widely commercially available. So, a public effort might focus on mining the patent literature, synthesizing various claimed compounds and verifying their activity. Of course, some (many?) compounds in the patents might not stand up to scrutiny. Another alternative would be to attempt to devise incentives for industry to release some of the inhibitors they have in house; obviously this would be a challenge as such compounds might prove to be the starting points for valuable drugs -- but of course they never will until someone proves the underlying kinases valueable. Some companies have generated unbelievable databases on kinase inhibitors (for example, this recent study) which have the potential to fill in the missing spots on the kinase tool compound grid.

I can't help thinking of the new translational medicine institute going in at the NIH. Trying to move research findings into the clinic to benefit patients is hard to argue against, but perhaps the NIH needs to also pour some resources into the humble task of finding basic tools.

Tuesday, February 08, 2011

Wrapping up AGBT

AGBT ended on Saturday, but both Saturday & Sunday were crammed with personal stuff. Monday night was some down time, so now tidying up.

Anthony Fejes has a nice final post on the meeting (along with all his useful notes); it's also interesting to see what a boost in traffic he gets for AGBT (and well deserved!). One very positive Twitter note: one presenter personally thanked him for blogging his talk; I know I get a thrill whenever authors visit this space with comments & it's good to see that sometimes blogging really is opening up a two-way conversation. A more constrained view on the proceedings can be seen in an investment house's research note.

A few last impressions of my own based on Anthony's notes and Twitter. Nanopores seem to be making progress -- but still quite distant from being able to generate any data. PacBio appears to have faced reality and is positioning themselves in areas where their strengths (read length, speed) are strengths and accepting that their per-base quality isn't going to be adequate for many applications. Metagenomics is something I really need to do a personal deep dive into -- it's often sounded cool & I'd love to know more. The whole idea that each region of my skin has a different flora is pretty amazing -- and one wonders what the scale of changes are (indeed, I wonder about how different my scales are than adjacent area -- it's winter and I have several serious dry patches). The Broad is using 500Gb of RAM on their machines doing de novo vertebrate assembly; given that my first and second computers came with 1Kb of RAM, that's pretty mind blowing.

Someone asked for my Twitter table. Alas, I didn't save some intermediate results & Twitter's search mechanism apparently now won't go back beyond Thursday night, but below is what I can spit out -- with the URLs turned into hyperlinks. Maybe before the next meeting I'll engage in some lily-gilding and have this thing build a SQLite database of results. Twitterstatistical summaries for the whole meeting are a bit interesting.

Tue, 08 Feb 2011 21:30:16 +0000 KamounLab¬タン AGBT Excellent summary: ¬タワ@genomeresearch: What investors heard at - summary & analysis from A Murphy of William Blair
Tue, 08 Feb 2011 18:57:00 +0000 genomicslawyer AGBT What investors heard at - summary & analysis from Amanda Murphy of William Blair:
Tue, 08 Feb 2011 12:07:24 +0000 samuellampa HTSeq,NextGenSeq,AGBT Or maybe is more time-proof (and shorter) than ...
Tue, 08 Feb 2011 12:05:30 +0000 samuellampa sequencing,NextGenSeq,AGBT (Seems clashes with some music production stuff etc ... )
Tue, 08 Feb 2011 12:04:43 +0000 samuellampa NextGenSeq #AGBT Folks, doesn't need a better hash tag? Some brainstorming? ...or what about the one above?
Mon, 07 Feb 2011 23:03:32 +0000 apfejes AGBT @PeroMHC is always at the same place on Marco Island.
Mon, 07 Feb 2011 22:47:05 +0000 PeroMHC AGBT Where is 2012??
Mon, 07 Feb 2011 22:16:49 +0000 finchtalk AGBT #1kgenome and now a chat Cliff Reed and Eric Schadt. From to Seattle. Luke Timmerman will moderate.
Mon, 07 Feb 2011 20:10:54 +0000 apfejes AGBT @drio Was it George Vacek, poster 214 in the book?
Mon, 07 Feb 2011 19:52:04 +0000 drio #AGBT does anyone remember the name of the company that had the poster about using FPGAs with velvet? or the person that presented.
Mon, 07 Feb 2011 18:23:55 +0000 bachinsky agbt @apfejes Thanks you for tweets
Mon, 07 Feb 2011 17:44:09 +0000 drjonboyg AGBT @apfejes thanks for writing up the sessions, your blog is a great resource.
Mon, 07 Feb 2011 17:39:10 +0000 apfejes AGBT Final thoughts and summary of this year's conference.
Mon, 07 Feb 2011 16:53:24 +0000 JVJAI AGBT @apfejes Thank you so much for your tweets & great meeting notes at
Mon, 07 Feb 2011 16:44:34 +0000 apfejes AGBT You're all welcome for the conf notes, @ntuseem, @ChaunceyGrattan, @genomeresearch, etc! I'm glad you're finding them to be useful!
Mon, 07 Feb 2011 16:31:58 +0000 PMedPartners agbt Check out the @twapperkeeper summary: 272 tweeters!
Mon, 07 Feb 2011 16:05:26 +0000 j3moore AGBT? @drjonboyg @djschlesinger: would you mind sharing what you found so impressive about the BioNanomatrix talk at
Mon, 07 Feb 2011 15:46:44 +0000 genomeresearch AGBT Genome Research back in Cold Spring Harbor. Thanks to all tweeps esp @apfejes @deannachurch @djschlesinger @drjonboyg @girlscientist
Mon, 07 Feb 2011 15:44:04 +0000 finchtalk #AGBT - once again, great conf. See photo for my summary.
Mon, 07 Feb 2011 13:02:10 +0000 deannachurch AGBT @drjonboyg thanks! And thanks to all of the tweeps for great feedback.
Mon, 07 Feb 2011 11:13:16 +0000 drjonboyg AGBT On reflection, a big thanks to @deannachurch and the other organizers, it was an excellent and informative meeting.
Mon, 07 Feb 2011 01:25:21 +0000 girlscientist AGBT Have to give recap of for lab mtg tomorrow. Now going to do it with lighted box on head.
Mon, 07 Feb 2011 00:47:11 +0000 girlscientist AGBT Back home -- thanks tweeps, it was a lot of fun. But snow forecast here tomorrow?!? Take me back to the beach....
Sun, 06 Feb 2011 21:21:38 +0000 deannachurch agbt,hoedown new in Roche sales.
Sun, 06 Feb 2011 19:25:09 +0000 ChaunceyGrattan AGBT @apfejes many thanks for the constant information stream. Future conf attendees should take note of how its done.
Sun, 06 Feb 2011 14:19:26 +0000 deannachurch AGBT,detox,sleep Bye-bye see you next year.
Sun, 06 Feb 2011 13:50:12 +0000 apfejes AGBT Apologies to Dr. Mungall, who's name has now been mispelled with one l all over the internet because I can't spell!
Sun, 06 Feb 2011 01:36:25 +0000 djschlesinger AGBT Are fish tacos traditional cowboy food?
Sun, 06 Feb 2011 01:28:56 +0000 omespeak AGBT The final swag: cowboy hats and bandanas at the dinner.
Sun, 06 Feb 2011 00:46:34 +0000 rforsberg AGBT Thanks for a great conference, see you next year at or see you at Copenhagenomics in June !! -
Sat, 05 Feb 2011 23:00:16 +0000 SOLiDSequencing sequencing #AGBT folks: want to stay up-to-date on @SOLiDSequencing news? Join the SOLiD Community:
Sat, 05 Feb 2011 22:54:34 +0000 SOLiDSequencing AGBT?,PGM Missed @LifeCorporation Triathlon Get the recap: Congrats to @iontorrent winner!
Sat, 05 Feb 2011 21:41:54 +0000 phylogenomics AGBT,sarcasm Basking in my brilliance for starting to track meeting during last talk
Sat, 05 Feb 2011 21:38:11 +0000 deannachurch AGBT Discussion on how people want to see improve. Suggestions?
Sat, 05 Feb 2011 21:37:28 +0000 rdeborja #AGBT last talk is now over. Met lots of people in the cancer genomics field.
Sat, 05 Feb 2011 21:37:15 +0000 phylogenomics AGBT,Experiment Alternative Real Time Twitter Feed for
Sat, 05 Feb 2011 21:37:01 +0000 djschlesinger AGBT Amazing meeting. Many thanks to the organizers. Only suggestion: would like to have had more time for posters.
Sat, 05 Feb 2011 21:35:01 +0000 apfejes AGBT After this talk, maybe Ellen Wright Clayton was right - you can go too far with sequencing!
Sat, 05 Feb 2011 21:32:17 +0000 girlscientist AGBT Schadt suggests we should all hook up PacBio machine to efflux from toilets so we can have health report on house occupants.
Sat, 05 Feb 2011 21:31:59 +0000 dsexton_2 agbt that may have been the scariest scenario ever presented
Sat, 05 Feb 2011 21:30:44 +0000 apfejes AGBT Waiting for announcement that Pac bio has collaborated with google to sequence your DNA as google maps & photographs you...
Sat, 05 Feb 2011 21:28:36 +0000 djschlesinger AGBT Pacific Biosciences SMRT + Illumina SBS = some damn cool data
Sat, 05 Feb 2011 21:27:41 +0000 deannachurch AGBT ES: having success combining Illumina and PacBio data.
Sat, 05 Feb 2011 21:26:32 +0000 phylogenomics AGBT Tracking Advances in Genome Biology & Technology meeting w/ Twitter Widget:
Sat, 05 Feb 2011 21:25:14 +0000 deannachurch AGBT ES: Profiling sewage as a proof of principle, because "Everybody poops".
Sat, 05 Feb 2011 21:22:30 +0000 girlscientist AGBT If you see someone in the airport bathroom looking crazy, it's just Eric Schadt sampling toilet flush handles for sequencing.
Sat, 05 Feb 2011 21:21:53 +0000 girlscientist AGBT Schadt: want to develop real-time disease weather map by viral metagenome sequencing of travel centers etc.
Sat, 05 Feb 2011 21:21:21 +0000 deannachurch AGBT ES: "Disease weather map" surveying viral metagenomes to try to predict outbreaks.
Sat, 05 Feb 2011 21:19:43 +0000 djschlesinger AGBT¬タン Has he taken a breath yet? ¬タワ@girlscientist: @apfejes no one, no one can keep up with Eric Schadt. You have done a great job.
Sat, 05 Feb 2011 21:19:16 +0000 deannachurch rapidfire,sorry,AGBT ES: Maybe the 93 contigs was just from Illumina/454- not sure-
Sat, 05 Feb 2011 21:18:02 +0000 deannachurch AGBT ES: Finishing and layering in Pac Bio- complete genome. 8 contigs >1Kb, 6 contigs covering 99% of genome.
Sat, 05 Feb 2011 21:17:40 +0000 girlscientist AGBT @apfejes no one, no one can keep up with Eric Schadt. You have done a great job.
Sat, 05 Feb 2011 21:17:06 +0000 apfejes finallydefeated,AGBT Cool talk from Pac Bio, but I just can't blog fast enough to keep up with the firehose of data presented.
Sat, 05 Feb 2011 21:16:47 +0000 deannachurch AGBT ES: 244X coverage in 454, Illumina and PacBio to do an assembly: still had 93 contigs after hybrid assembly.
Sat, 05 Feb 2011 21:16:26 +0000 girlscientist AGBT Schadt et al. have gone on from NEJM paper to combine Illumina, PacBio regular, and PacBio strobed sequence reads to complete genomes.
Sat, 05 Feb 2011 21:13:55 +0000 deannachurch AGBT ES: sequence in 90 minutes, then on to the comparative genomes; "quick as serotyping or fingerprinting".
Sat, 05 Feb 2011 21:11:36 +0000 djschlesinger AGBT Eric: Cholera strain to sequence data (on PacBio) to published paper in 4 weeks!!
Sat, 05 Feb 2011 21:07:22 +0000 djschlesinger AGBT @apfejes for long term sustainability, I agree. However I think sugar cane would be ideal to fill an immediate need.
Sat, 05 Feb 2011 21:07:00 +0000 djschlesinger AGBT Eric Schadt from PacBio on rapid pathogen ID.
Sat, 05 Feb 2011 21:06:54 +0000 deannachurch AGBT ES: OK- two minutes in and very cool visualization...
Sat, 05 Feb 2011 21:05:14 +0000 deannachurch AGBT Eric Schadt to end the day: sequencing for impacting health.
Sat, 05 Feb 2011 21:05:10 +0000 girlscientist AGBT Last talk of = Eric Schadt and PacBio's cholera work.
Sat, 05 Feb 2011 21:04:29 +0000 girlscientist AGBT Zhong Wang offers ftp address for data, "if you want to stick your hand in cow rumen and see what you get out." Check JGI site.
Sat, 05 Feb 2011 21:03:36 +0000 SEQanswers agbt Ah the fistulated cow, brings back memories of UC Davis!
Sat, 05 Feb 2011 21:03:18 +0000 apfejes AGBT Notes and thoughts on Zhong Wang's talk on cow gut microbiome + cellulases:
Sat, 05 Feb 2011 21:02:21 +0000 djschlesinger AGBT good point, was thinking biological: @mlb_house: @djschlesinginger or, how about improving solar panels and directly harvesting solar?
Sat, 05 Feb 2011 21:01:39 +0000 apfejes AGBT @djschlesinger Sugar cane still produces a lot of cellulosic waste - it's better to use the cellulose than compete for the glucose.
Sat, 05 Feb 2011 21:00:44 +0000 mlb_house AGBT @djschlesinginger or, how about improving solar panels and directly harvesting solar?
Sat, 05 Feb 2011 20:59:52 +0000 MaliciaRogue AGBT . ¬ルᄏ @genomeresearch: JGI cow rumen metagenome assembly by Velvet
Sat, 05 Feb 2011 20:59:21 +0000 deannachurch AGBT Wang: Doing single cell sequencing to try to validate assemblies from metagenomes.
Sat, 05 Feb 2011 20:57:39 +0000 genomeresearch AGBT JGI cow rumen metagenome assembly by Velvet
Sat, 05 Feb 2011 20:52:51 +0000 djschlesinger AGBT Instead of finding or engineering enzymes to turn cellulose to sugar, why not engineer sugar cane to grow in more temperate climates?
Sat, 05 Feb 2011 20:48:46 +0000 djschlesinger AGBT @apfejes I believe switchgrass yields more energy than corn per equal mass.
Sat, 05 Feb 2011 20:46:11 +0000 deannachurch AGBT @apfejes switchgrass is cheaper to grow- and it is not a human food source so you don't create price competition.
Sat, 05 Feb 2011 20:45:20 +0000 SOLiDSequencing PGM,AGBT Congrats to Adam English, Baylor, winner of @iontorrent sequencer. $10K ($1/total points) goes to Komen for the Cure!
Sat, 05 Feb 2011 20:45:09 +0000 apfejes AGBT Odd that switchgrass was used - it's grows fast, but corn cellulose or other grass stalks are plentiful as a wasteproduct...
Sat, 05 Feb 2011 20:41:17 +0000 deannachurch AGBT Wang: JGI has a cow with a "door" so they can efficiently sample rumen.
Sat, 05 Feb 2011 20:41:10 +0000 SOLiDSequencing AGBT,sequencing @apfejes really enjoying your live blogging (where allowed). Thanks for the great conference notes.
Sat, 05 Feb 2011 20:39:46 +0000 cslamo #AGBT folks stop RTing BS or I'll unfollow everyone!
Sat, 05 Feb 2011 20:36:22 +0000 deannachurch AGBT Zhong Wang: using genomics to address our fuel needs.
Sat, 05 Feb 2011 20:34:18 +0000 apfejes AGBT Rather incomplete notes on Mark Akeson's (movie filled) talk on nanopores:
Sat, 05 Feb 2011 20:33:01 +0000 girlscientist AGBT Next talk: Zhong Wang, JGI, metagenomics of cow rumen. Just published in Science.
Sat, 05 Feb 2011 20:32:24 +0000 girlscientist AGBT Akeson: next steps include seq and re-seq indiv DNA templates, and generating read-lengths signif. longer than industry standards.
Sat, 05 Feb 2011 20:29:16 +0000 nanopore AGBT MA: phi29 high processivity and catalysis rate, animation representing data from JACS paper
Sat, 05 Feb 2011 20:24:40 +0000 nanopore AGBT MA: movie - watching Klenow fragment add bases. Trace showing measurement of ionic current
Sat, 05 Feb 2011 20:23:52 +0000 KamounLab AGBT Link to Lorena Beese's movie "processive DNA synthesis in a polymerase crystal" mentioned by Mark Akeson
Sat, 05 Feb 2011 20:18:10 +0000 nanopore AGBT MA: how to control translocation of ssDNA through a nanopore..add a processive enzyme. up first Klenow fragment
Sat, 05 Feb 2011 20:16:09 +0000 girlscientist AGBT Akeson: group of Jens Gundlach doing promising work on changing over from alpha-hemolysin nanopore to MspA.
Sat, 05 Feb 2011 20:13:45 +0000 nanopore AGBT MA: Bayley group's recognition of bases inc modified bases on a strand
Sat, 05 Feb 2011 20:13:04 +0000 nanopore AGBT MA: in wild type hemolysin, many bases contribute to signal - so engineering of reader heads needed for resolution
Sat, 05 Feb 2011 20:11:42 +0000 djschlesinger AGBT Protein nanopores seem to offer more flexibility that solid state. With mutagenesis, you can get them to do almost anything.
Sat, 05 Feb 2011 20:09:23 +0000 girlscientist AGBT Mark Akeson, UCSC: strand sequencing through nanopores. I am going to defer to @nanopore for tweeting details.
Sat, 05 Feb 2011 20:08:27 +0000 rforsberg agbt Allpaths-lg needs 500 Gb memory to assemble a vertebrate genome
Sat, 05 Feb 2011 20:06:49 +0000 nanopore AGBT MA: reagents: 100ml ocean water and the air we breathe
Sat, 05 Feb 2011 20:05:22 +0000 nanopore AGBT Mark Akeson, UCSC: two types of nanopore DNA seq: exonuclease and strand. His talk about strand
Sat, 05 Feb 2011 20:05:11 +0000 apfejes AGBT Notes on David Jaffe's talk on assembly (allpaths-lg) :
Sat, 05 Feb 2011 20:04:22 +0000 deannachurch AGBT Mark Akeson: on Nanopores!
Sat, 05 Feb 2011 20:04:01 +0000 bffo AGBT Ok boys and girls, I'm out of here! It was a fun meeting, and I enjoyed the tweets, and I like where tweeting will be next year!
Sat, 05 Feb 2011 20:02:14 +0000 deannachurch AGBT @djschlesinger de novo gets you insertions, inversions and translocations too- really is the best way to understand variation.
Sat, 05 Feb 2011 19:59:44 +0000 bffo AGBT Did Jaffe just say: if it is in genbank it must be real? :-)
Sat, 05 Feb 2011 19:59:43 +0000 djschlesinger AGBT de novo assembly identifies things (large deletions only?) not found any other way
Sat, 05 Feb 2011 19:58:33 +0000 girlscientist AGBT Take note kids, that's the pickup line for the hoe-down tonight, "don't you want to fully know my genome?"
Sat, 05 Feb 2011 19:58:08 +0000 girlscientist AGBT Jaffe, We all should be interested in denovo assembly "to fully know a person's genome."
Sat, 05 Feb 2011 19:57:11 +0000 deannachurch AGBT @djschlesinger It is the technical term!
Sat, 05 Feb 2011 19:56:47 +0000 djschlesinger AGBT Is "crappy" a quantitative term
in bioinformatics?
Sat, 05 Feb 2011 19:52:27 +0000 KamounLab AGBT Genome Biol "Analyzing and minimizing bias in Illumina sequencing libraries"
Sat, 05 Feb 2011 19:51:22 +0000 girlscientist AGBT David Jaffe offering detailed comparisons of genome metrics by multiple assembly algorithms. Somebody's gotta do it.
Sat, 05 Feb 2011 19:50:03 +0000 genomeresearch AGBT SOAPdenovo
Sat, 05 Feb 2011 19:49:38 +0000 djschlesinger AGBT Anyone have a copy of "bioinformatics for dummies" that I can borrow?
Sat, 05 Feb 2011 19:48:11 +0000 deannachurch AGBT @girlscientist yes- that is what I heard...
Sat, 05 Feb 2011 19:46:21 +0000 girlscientist AGBT Did David Jaffe just say currently ~1week for 1Gb of genome?
Sat, 05 Feb 2011 19:46:15 +0000 GenomeRef AGBT DJ: AllPathsLG- still needs significant computational power and memory: can assemble about 1G per week.
Sat, 05 Feb 2011 19:46:07 +0000 new299 AGBT ALLPATHS LG running on 512Gb node for human assemblies, ouch + want!
Sat, 05 Feb 2011 19:44:28 +0000 GenomeRef AGBT DJ: Representing variation- recognizing that one path is not representative of biology.
Sat, 05 Feb 2011 19:41:32 +0000 djschlesinger AGBT Jaffe: method to increase read length is to connect 100bp paired end reads with a 3rd overlapping read from data set
Sat, 05 Feb 2011 19:37:50 +0000 deannachurch AGBT DJ: Need both technology improvements and algorithmic improvements to succeed.
Sat, 05 Feb 2011 19:37:36 +0000 djschlesinger AGBT Jaffe: de novo assembly with short reads requires new computational and new laboratory methods.
Sat, 05 Feb 2011 19:37:23 +0000 new299 AGBT ALLPATHS LG using specific lab protocol.
Sat, 05 Feb 2011 19:37:05 +0000 GenomeRef AGBT First up: David Jaffe talking about a subject we love: Genome assemblies!
Sat, 05 Feb 2011 19:36:27 +0000 girlscientist AGBT David Jaffe, Broad Inst: Goal = each new genome is not a research project. Hmmmm.
Sat, 05 Feb 2011 19:32:54 +0000 djschlesinger AGBT David Jaffe (Broad) discussing high quality draft assembly of vert genomes with NGS data
Sat, 05 Feb 2011 19:32:13 +0000 apfejes AGBT yay... more tweeting allowed for all speakers this session!
Sat, 05 Feb 2011 19:32:09 +0000 deannachurch AGBT Last session: "Genomic Frontiers" and all are tweetable!
Sat, 05 Feb 2011 19:11:12 +0000 apfejes AGBT Argh... "we searchable" should be "web searchable" notes. You'd think I'd have some practice typing by now with all that blogging.
Sat, 05 Feb 2011 19:06:47 +0000 apfejes AGBT hah. I need error correction on my tweets about error rats... or a cage to keep them in. thanks @nilshomer
Sat, 05 Feb 2011 19:04:57 +0000 apfejes AGBT @KamounLab As I said, I really enjoyed hearing it, and the blogging part just means I get we searchable notes. (-:
Sat, 05 Feb 2011 19:04:14 +0000 apfejes AGBT Any time I'm within 2m of a windows computer, the wireless becomes unreliable... coincidence?
Sat, 05 Feb 2011 18:56:04 +0000 KamounLab AGBT @apfejes Thanks for live blogging my talk. Was fun to read your notes!
Sat, 05 Feb 2011 18:53:39 +0000 drjonboyg AGBT Off to the airport. Have safe trips home, twitterers.
Sat, 05 Feb 2011 18:39:46 +0000 omespeak AGBT? @nanopore Are you by any chance showing the system at this
Sat, 05 Feb 2011 18:39:26 +0000 halletecco agbt Thank you planning committee for picking such a phenomenal location!
Sat, 05 Feb 2011 18:20:14 +0000 neilhall_uk agbt @djschlesinger I thought I stepped into the wrong meeting?
Sat, 05 Feb 2011 18:15:07 +0000 nanopore AGBT If you didn't see the electronics platform that underlies Oxford Nanopore's single mol sensing: GridION
Sat, 05 Feb 2011 18:13:38 +0000 djschlesinger AGBT Must have walking into wrong room, talk seems to be about ant colonies??
Sat, 05 Feb 2011 18:11:34 +0000 djschlesinger AGBT Late to 454 workshop, don't know who's speaking.
Sat, 05 Feb 2011 17:59:41 +0000 djschlesinger AGBT Modified bases change the kinetics and the subsequent base call.
Sat, 05 Feb 2011 17:58:44 +0000 djschlesinger AGBT Steve back quickly discussing future directions in detecting modified bases.
Sat, 05 Feb 2011 17:52:25 +0000 djschlesinger AGBT Accuracy was improved to 99% with circular coverage, but read length is severely limited.
Sat, 05 Feb 2011 17:50:58 +0000 djschlesinger AGBT Gen-Probe was able to detect variants with 1% frequency with deep resequencing
Sat, 05 Feb 2011 17:49:16 +0000 djschlesinger AGBT 85% accuracy seems fixed, wonder if they've hit the threshold with single molecule sequencing technology.
Sat, 05 Feb 2011 17:43:42 +0000 djschlesinger AGBT Matt Friedenberg from Gen-Probe up next.
Sat, 05 Feb 2011 17:42:29 +0000 djschlesinger AGBT Requires micrograms of starting material. :(
Sat, 05 Feb 2011 17:42:22 +0000 apfejes AGBT did I get that right? Pac Bio has problems with GC, but was that before or after their new chemistry that fixes GC homopolymers
Sat, 05 Feb 2011 17:42:01 +0000 nanopore AGBT pm session starts 2.30, then 3pm Oxford Nanopore collaborator Mark Akeson on his work at UCSC. Focus: translocation of ssDNA thru pore
Sat, 05 Feb 2011 17:41:43 +0000 djschlesinger AGBT Bias summary: No amplification bias, but limited coverage bias.
Sat, 05 Feb 2011 17:40:31 +0000 djschlesinger AGBT coverage is consistently random across genome, but dips a bit in higher GC genomes
Sat, 05 Feb 2011 17:38:07 +0000 djschlesinger AGBT Accuracy does not decrease with read length, 85% accuracy holds out to 6kb.
Sat, 05 Feb 2011 17:36:57 +0000 djschlesinger AGBT JGI observed no GC bias out to ~85% GC
Sat, 05 Feb 2011 17:36:46 +0000 apfejes AGBT,makessense Interesting changes in Pac Bio's story this year: lower accuracy is acceptable - use platform in combination with others.
Sat, 05 Feb 2011 17:35:55 +0000 djschlesinger AGBT JGI confirms average 1.5kb read length, with longer reads out to 6kb!
Sat, 05 Feb 2011 17:33:03 +0000 djschlesinger AGBT Len Pennacchio (JGI) talking about closing gaps is microbial genome sequences with PacBio platform
Sat, 05 Feb 2011 17:27:31 +0000 djschlesinger AGBT higher error rates are tolerated better when mapping longer reads (>500kb)
Sat, 05 Feb 2011 17:25:26 +0000 djschlesinger AGBT 1Kb read with 10% error maps like a 740bp read
Sat, 05 Feb 2011 17:24:14 +0000 djschlesinger AGBT Couldn't find an alignment algorithm what could support long read lengths with indels, so the designed their own
Sat, 05 Feb 2011 17:21:30 +0000 djschlesinger AGBT Single molecule sequencing platforms dominated by insertion/deletion errors. As expected.
Sat, 05 Feb 2011 17:16:54 +0000 djschlesinger AGBT John Sorenson (PacBio) discussing informatics of their recent Cholera project
Sat, 05 Feb 2011 17:15:03 +0000 djschlesinger AGBT Commercial release expected to have 35-45Mb of mappable data
Sat, 05 Feb 2011 17:13:18 +0000 djschlesinger AGBT Will have an output of 22Mb per run
Sat, 05 Feb 2011 17:12:19 +0000 girlscientist AGBT At PacBio workshop.
Sat, 05 Feb 2011 17:11:49 +0000 djschlesinger AGBT PacBio machine will have average 1.5kb reads on commercial release, with 85% accuracy
Sat, 05 Feb 2011 17:10:02 +0000 djschlesinger AGBT 3rd gen single molecule platforms will have inherently higher error compared to 2nd gen, which looks at an average over many molecules
Sat, 05 Feb 2011 17:06:10 +0000 djschlesinger AGBT Steve Turner up discussing recent advances in PacBio technology.
Sat, 05 Feb 2011 17:02:53 +0000 djschlesinger AGBT Farewell to those Tweeps departing today. Hope you make it back safe and on time. Was a pleasure Tweeting with you.
Sat, 05 Feb 2011 16:57:19 +0000 djschlesinger AGBT Pacific Biosciences workshop about to start, hoping to see some real data!
Sat, 05 Feb 2011 16:54:48 +0000 suganthibala AGBT. Thanks to all tweeters from the forbidden zone :)
Sat, 05 Feb 2011 16:54:00 +0000 omespeak AGBT
Where the conference attendees spend time when not at a session:
Sat, 05 Feb 2011 16:51:58 +0000 omespeak AGBT Where the conference attendees spend time when not at a session:
Sat, 05 Feb 2011 16:50:41 +0000 apfejes AGBT We're slowly coming to the end of the talks, with only a few more to go this aft, but thanks to everyone for the RTs!
Sat, 05 Feb 2011 16:47:26 +0000 apfejes AGBT Notes on AGBT talk: Sophien Kamoun on potato pathogens:
Sat, 05 Feb 2011 16:37:08 +0000 dwmohr AGBT Wondering what/who will repopulate my microbiome once I'm done my antibiotics
Sat, 05 Feb 2011 16:19:24 +0000 omespeak AGBT Interesting variety of talks this morning: from gut micobiome to potato famine pathogens.
Sat, 05 Feb 2011 16:18:14 +0000 new299 AGBT Am I allowed to take pictures of drawings of slides?
Sat, 05 Feb 2011 16:17:14 +0000 apfejes AGBT Notes on James Giovannoni's talk on the Tomato Genome:
Sat, 05 Feb 2011 16:09:02 +0000 drjonboyg AGBT Apparently several people saw my name in one of John Oliver's (NABsys) slides. No idea how, wonder if he'd give me a copy?
Sat, 05 Feb 2011 16:06:20 +0000 drjonboyg AGBT @nanopore well, I was at that talk so I really should have noticed it was Gundlach and not Akeson! Will follow the talk at the airport
Sat, 05 Feb 2011 16:06:06 +0000 bffo AGBT James Giovannoni talking about closing gaps with ngs data, referee to IMAGE software
Sat, 05 Feb 2011 16:03:45 +0000 GenomeRef AGBT JG: working to make a 'gold standard' tomato genome!
Sat, 05 Feb 2011 16:02:13 +0000 nanopore AGBT @dijonboyg @omespeak Jens Gundlach spoke Thursday (as you say MspA pores) and Mark Akeson was moved to Sat.
Sat, 05 Feb 2011 15:59:11 +0000 drjonboyg AGBT @nanopore @omespeak Akeson also spoke on Thursday, didn't he? (MspA pores).
Sat, 05 Feb 2011 15:55:42 +0000 drjonboyg AGBT I think there might be a candidate for LATFH here at (although he maybe saying the same thing about me)
Sat, 05 Feb 2011 15:55:38 +0000 GenomeRef AGBT James Giovannoni talking about sequencing the tomato genome. Started BAC by BAC, now adding NGS
Sat, 05 Feb 2011 15:54:52 +0000 omespeak AGBT After Rob Knight's talk this morning, am wondering what microbes get transferred to my fingers when using a public computer.
Sat, 05 Feb 2011 15:48:31 +0000 apfejes AGBT We've been reminded that photography of slides is not allowed - but does U2 count?
Sat, 05 Feb 2011 15:44:39 +0000 new299 AGBT U2 at
Sat, 05 Feb 2011 15:38:12 +0000 drjonboyg AGBT Although actually it's not even from @nanopore ()
Sat, 05 Feb 2011 15:35:20 +0000 apfejes AGBT For entertainment, some analytics data for my blog during season:
Sat, 05 Feb 2011 15:34:59 +0000 drjonboyg AGBT Rather bummed that the only talk I have any interest in seeing today (@nanopore) is on after I need to head to the airport.
Sat, 05 Feb 2011 15:23:23 +0000 KirstinWrites AGBT @drjonboyg I'm not at the conference ... but I agree with the statement.
Sat, 05 Feb 2011 15:11:49 +0000 omespeak AGBT Baylor U heavily invested solving the viral metageome of Elephant Herpes Virus as a step towards cure.
Sat, 05 Feb 2011 15:11:47 +0000 girlscientist AGBT Both Knight & Petrosino agreed with audience Q that w/their strategies, we'd miss viral/bacterial genomes w/weird, non-seq'able bases.
Sat, 05 Feb 2011 15:11:39 +0000 apfejes AGBT Notes on Joseph Petrosino's talk on Viral metagenomics:
Sat, 05 Feb 2011 15:09:46 +0000 omespeak AGBT Practical application of viral metagenomics: develop therapy for Elephant Herpes virus that kills Asian baby elephants.
Sat, 05 Feb 2011 15:09:25 +0000 drjonboyg AGBT One more good use of twitter at conferences: an excellent way of meeting people.
Sat, 05 Feb 2011 15:08:42 +0000 obahcall AGBT Petrosino: Virus protocol is able to differentiate stool and nasal wash samples. We can tell our nose from our rear.
Sat, 05 Feb 2011 15:05:54 +0000 omespeak AGBT How to tell the difference between your nose & other end? Different virus exist in stool & nasal washes -J Petrosino.
Sat, 05 Feb 2011 15:05:29 +0000 new299 AGBT Nose v arse detection via microbiome sequencing
Sat, 05 Feb 2011 15:05:24 +0000 girlscientist AGBT Sorry tweeps wifi just died so radio silence ensuing.
Sat, 05 Feb 2011 15:04:34 +0000 bffo AGBT JP "pretty cool that the phage can tell you which bacteria re there"
Sat, 05 Feb 2011 15:02:44 +0000 new299 AGBT Random primers for looking at microbiome...
Sat, 05 Feb 2011 15:01:31 +0000 obahcall AGBT Petrosino: What does your poo tell you? Looking at representation of DNA/RNA virsues in stool.
Sat, 05 Feb 2011 14:58:23 +0000 obahcall AGBT Joseph Petrosino: Overview of NIH¬タルs Human microbiome project, showing bacterial communities differ at different body sites.
Sat, 05 Feb 2011 14:57:28 +0000 bffo AGBT HMP data is so fresh, it is "dripping wet" JP
Sat, 05 Feb 2011 14:56:24 +0000 obahcall AGBT Knight: Shows a memorable visualization following the distribution of bacteria across human face.
Sat, 05 Feb 2011 14:56:13 +0000 girlscientist AGBT Joe Petrosino showing figure of vaginal viral microbiomes, with two different collection methods called "swab" & "broom." Eek.
Sat, 05 Feb 2011 14:55:29 +0000 bffo AGBT,HMP @girlscientist what about the biofilm on my iPad?
Sat, 05 Feb 2011 14:52:34 +0000 bffo AGBT Joe Petrosino gave intro to NIH's Human Microbiome project and also viruses ...
Sat, 05 Feb 2011 14:52:33 +0000 girlscientist AGBT [now paranoid about pushing my glasses up on my nose and introducing fingertip bacteria to site.]
Sat, 05 Feb 2011 14:48:05 +0000 girlscientist AGBT J Petrosino: human microbiome project, multiple sides probed in ¬タワworst doctor¬タルs appointment ever¬タン for subjects.
Sat, 05 Feb 2011 14:47:12 +0000 obahcall AGBT Rob Knight: Overview microbiome studies, open microbiome initiative, partnership with Gates for pers medicine in developing nations.
Sat, 05 Feb 2011 14:45:34 +0000 omespeak AGBT Joseph Petrosino: very hard to follow a talk that is probably trending on twitter.
Sat, 05 Feb 2011 14:42:55 +0000 omespeak AGBT Very entertaining talk by R Knight on microbiome diversity, especially his digression into the Onion-like NGS techniques too look for.
Sat, 05 Feb 2011 14:42:00 +0000 apfejes AGBT Notes on Rob Knight's talk on the Human Microbiome:
Sat, 05 Feb 2011 14:41:41 +0000 new299 AGBT Microbiome and genetics linked in fat mice
Sat, 05 Feb 2011 14:39:53 +0000 girlscientist AGBT Rob Knight mentions Open Microbiome Initative,
Sat, 05 Feb 2011 14:38:18 +0000 omespeak AGBT Personalized medicine in developing nations based on microbial diversity?
Sat, 05 Feb 2011 14:33:57 +0000 girlscientist AGBT R Knight: lovely visualizations of which bacteria are on which parts of the face, but this reveals subject's habits, shall we say.
Sat, 05 Feb 2011 14:32:20 +0000 omespeak AGBT Just born babies have different microbiomes depending on normal vs c-section birth.
Sat, 05 Feb 2011 14:30:26 +0000 omespeak AGBT Wow! the biogeography of the human face is varied too, but symmetrical.
Sat, 05 Feb 2011 14:27:10 +0000 omespeak AGBT Microbiome habitats are very different in different parts of the body; also changes with time. Rob Knight
Sat, 05 Feb 2011 14:24:57 +0000 SEQanswers agbt Hopefully someone is capturing Rob Knights jokes, they are great and I can't type that fast
Sat, 05 Feb 2011 14:24:46 +0000 girlscientist AGBT Rob Knight certainly a comedian. Treating us to four proposed sequencing technologies to work out for, including unicorns.
Sat, 05 Feb 2011 14:22:51 +0000 omespeak AGBT Rob Knight: why is it called 454? It's the temp at which money burns for sequencing. :)
Sat, 05 Feb 2011 14:20:47 +0000 omespeak AGBT Micriobiomes in extreme environments are interestingly not outliers.
Sat, 05 Feb 2011 14:17:45 +0000 girlscientist AGBT Rob Knight: his keyboard microbiome study published in PNAS but then featured on CSI: Miami ¬タワso you really know it¬タルs true.¬タン
Sat, 05 Feb 2011 14:16:36 +0000 omespeak AGBT Rob Knight: each of us have an unique microbiome on fingertips that is transferred to computer keys.
Sat, 05 Feb 2011 14:13:54 +0000 girlscientist AGBT Rob Knight, UC Boulder: Problem of microbiome sequencing = get big phylogenetic trees which are hard to understand and analyze.
Sat, 05 Feb 2011 14:09:24 +0000 omespeak AGBT Rob Knight: Microbial symbionts are like unique snowflakes ie more varied than human genes.
Sat, 05 Feb 2011 14:07:35 +0000 djschlesinger AGBT Need a break, will pick up after lunch.
Sat, 05 Feb 2011 14:06:28 +0000 djschlesinger AGBT @mbcf, 8 hrs from sample to data, 5min per base, ALL reagents in single cartridge, no cBot or PE module needed, possible 510k approval
Sat, 05 Feb 2011 14:03:05 +0000 apfejes AGBT Yay! All four presenters this morning can be tweeted/blogged.
Sat, 05 Feb 2011 13:53:01 +0000 apfejes AGBT If anyone lost a pair of glasses last night, it's been turned in to reception. (but can you read this tweet?)
Sat, 05 Feb 2011 13:38:46 +0000 mbcf AGBT. Wake Up MiSeq: just a HiSeq Mini Me or something more? Blog on what you think is so clever about this box. "I want one." And ...
Sat, 05 Feb 2011 07:24:00 +0000 SOLiDSequencing PGM,AGBT Adam English of Baylor wins @iontorrent sequencer @ @LifeCorporation Triathlon. Congrats, Adam!
Sat, 05 Feb 2011 06:25:45 +0000 davcraig #AGBT
Sat, 05 Feb 2011 05:09:56 +0000 drjonboyg AGBT @genomicslawyer @lukejostins @mndoci in defense, it's not a default no tweet policy, its up to individual speakers.
Sat, 05 Feb 2011 04:42:14 +0000 drjonboyg AGBT OK, really going to bed now.
Sat, 05 Feb 2011 04:36:57 +0000 LIFECorporation AGBT Adam English of Baylor College of Medicine wins the PGM at the Life Technology Triathlon at Congrats!
Sat, 05 Feb 2011 03:34:49 +0000 girlscientist AGBT Mini tweetup with @deannachurch and @bffo in lobby bar. Stop by!
Sat, 05 Feb 2011 03:18:34 +0000 drjonboyg AGBT Calling it a night. Here's a video of the beach fireworks to keep you occupied.
Sat, 05 Feb 2011 01:53:55 +0000 apfejes AGBT Neat mechanism of disease in the Clinical Sequencing session, but I can't talk about it. DOH! only 56 people get to hear about it.
Sat, 05 Feb 2011 01:52:29 +0000 omespeak AGBT Last talk of the day on Cloud solutions for genomic data storage/transfer. Not doing the answer is 'cloudy since we can't tweet' jokes
Sat, 05 Feb 2011 01:52:26 +0000 dsexton_2 #agbt The Broad is testing their pipelines on Amazon. They will be optimizing Picard for the cloud.
Sat, 05 Feb 2011 01:45:45 +0000 drjonboyg AGBT There seem to be a certain irony in someone presenting on cloud computing but not allowing social media.
Sat, 05 Feb 2011 01:36:46 +0000 apfejes AGBT Notes on Praveen Cherukuri's talk on allele specific expression
Sat, 05 Feb 2011 01:26:02 +0000 dsexton_2 #agbt everyone needs to "value add" for their cores.
Sat, 05 Feb 2011 01:24:55 +0000 SEQanswers AGBT,badbatterylifebutwhocares During this break...I must express that I have a severe case of Macbook Air envy. I'm surrounded by them.
Sat, 05 Feb 2011 01:20:08 +0000 apfejes AGBT Notes from Kateryna Makova's excellent talk on Mitochondria heteroplasmy
Sat, 05 Feb 2011 01:18:41 +0000 dwmohr core,AGBT Why is 'core' not enough? ++
Sat, 05 Feb 2011 01:07:37 +0000 drjonboyg AGBT Is nuclear transfer from one oocyte to another even legal? Seems like the sort of thing bioconservatives freak out over.
Sat, 05 Feb 2011 01:02:46 +0000 deannachurch fail,agbt Session chair
Sat, 05 Feb 2011 00:58:28 +0000 girlscientist AGBT Marc Allard, FDA: no tweetability announced so will just say that the man clearly has difficult problems to solve. Cheers to him.
Sat, 05 Feb 2011 00:54:43 +0000 new299 AGBT Baylor sequencers + 3 ion torrent + Pacbio.
Sat, 05 Feb 2011 00:53:25 +0000 Mikegenome agbt Did I read that right that 6 illuminas = 30 SOLiDs at Baylor? Musny
Sat, 05 Feb 2011 00:47:32 +0000 new299 AGBT More ion torrent error rates, lots of things less than Q17?
Sat, 05 Feb 2011 00:41:31 +0000 SOLiDSequencing PGM!,AGBT In it to win it? Anyone could go home w/ the @iontorrent @LifeCorporation Triathlon NOW (5-9 pm), Suite 1106.
Sat, 05 Feb 2011 00:40:14 +0000 new299 AGBT Ion torrent run reports
Sat, 05 Feb 2011 00:37:21 +0000 apfejes AGBT Notes on Daniel Neafsey's talk on sequencing parasite genomes:
Sat, 05 Feb 2011 00:36:15 +0000 drjonboyg AGBT Horrible AV feedback in the clinical session.
Sat, 05 Feb 2011 00:33:18 +0000 djschlesinger AGBT Joe Boland from NCI is wearing a t-shirt that says "Tweet Me" in huge letters. Speaking on Ion Torrent's PGM.
Sat, 05 Feb 2011 00:32:09 +0000 SEQanswers AGBT Boland: Giant T-shirt "TWEET ME"
Sat, 05 Feb 2011 00:29:23 +0000 girlscientist AGBT Neafsey and Broad colleagues make their own whole genome bait oligos from malaria parasite DNA.
Sat, 05 Feb 2011 00:25:09 +0000 new299 AGBT I vote that all simulated data has this banner from now on
Sat, 05 Feb 2011 00:23:11 +0000 new299 AGBT Errr that looks weird, polyC artefact reads?
Sat, 05 Feb 2011 00:22:20 +0000 girlscientist AGBT Daniel Neafsey, Broad: sequencing of pathogen genomes from human clinical samples, without culturing them.
Sat, 05 Feb 2011 00:21:03 +0000 new299 AGBT Thinks after fiddlings as good as PCR free
Sat, 05 Feb 2011 00:20:29 +0000 apfejes AGBT Nice talk by Matthew Bainbridge, (Clinical seq session), but same (untwitterable) story told by others. Missed the twitter status too
Sat, 05 Feb 2011 00:17:03 +0000 new299 AGBT Effect of Pcr on GC bias
Sat, 05 Feb 2011 00:14:40 +0000 girlscientist AGBT The elevators made me a minute late so I missed what the lovely @deannachurch announced about tweeting policy in her clinical session.
Fri, 04 Feb 2011 23:40:10 +0000 SOLiDSequencing PGM!,AGBT It's a tight race... anyone could go home w/ the @iontorrent @LifeCorporation Triathlon 5-9 pm, Suite 1106.
Fri, 04 Feb 2011 23:15:00 +0000 drjonboyg AGBT Just watched the sun set over the ocean. Haven't been able to do that since I lived in Encinitas.
Fri, 04 Feb 2011 23:10:14 +0000 ChaunceyGrattan HiSeq2000.,agbt @Lyro20 re: David Bently & 1Tbp from How did they increase output? increased cluster density?
Fri, 04 Feb 2011 22:55:46 +0000 djschlesinger AGBT Just got to check out the MiSeq in person. The design was thoroughly thought out. An amazing instrument! Can't wait to get one!
Fri, 04 Feb 2011 22:07:28 +0000 bioinfosm AGBT Broad Institute is seemingly devoting 42 CPUs to processing data from each of its HiSeqs - heard from
Fri, 04 Feb 2011 21:37:57 +0000 Lyro20 AGBT¬タン #Norseqcenter ¬タワDavid Bentley: illumina HiSeq2000 exceeding 1 TERABASE sequence/run (up from 200 Gb launch spec 12 months ago).
Fri, 04 Feb 2011 21:36:10 +0000 SOLiDSequencing SOLiD,AGBT. @LifeCorporation Workflow Automation: AB Library Builder featured at
Fri, 04 Feb 2011 21:28:53 +0000 SOLiDSequencing http://t CE,sequencing,AGBT @LifeCorporation 3500 Genetic Analyzer, gold standard in capillary electrophoresis.
Fri, 04 Feb 2011 21:26:09 +0000 SOLiDSequencing SOLiD,AGBT,sequencing 5500 Series Sequencer featured in @LifeCorporation Suite at
Fri, 04 Feb 2011 21:11:51 +0000 apfejes AGBT Notes from Ion Torrent Talk ... off to the tweetup! See you there
Fri, 04 Feb 2011 21:11:42 +0000 SOLiDSequencing AGBT,sequencing Introducing... the @iontorrent PGM¬トᄁ sequencer, "Personal Genome Machine".
Fri, 04 Feb 2011 21:11:34 +0000 KamounLab AGBT Chad Nusbaum on Ion Torrent: very low GC bias with E. coli, accuracy uniform too, less bias than other technologies
Fri, 04 Feb 2011 21:10:04 +0000 SEQanswers AGBT @drjonboyg @apfejes IonT/Broad talk still going on.
Fri, 04 Feb 2011 21:08:29 +0000 apfejes AGBT. @drjonboyg Talk should be over in a couple minutes, and several of us will be there
Fri, 04 Feb 2011 21:06:50 +0000 drjonboyg AGBT @apfejes I think I'm the only person here.
Fri, 04 Feb 2011 21:06:40 +0000 KamounLab AGBT Chad Nusbaum on Ion Torrent applications: mutation validation, targeted resequencing, QC nextgen libraries, resequencing microbes...
Fri, 04 Feb 2011 21:00:04 +0000 djschlesinger AGBT Chad Nusbaum (Broad) about to show some new Ion Torrent data.
Fri, 04 Feb 2011 20:57:30 +0000 SOLiDSequencing AGBT @LifeCorporation Triathlon REGISTRATION: BE THERE Fri. 5-9pm Suite 1106!
Fri, 04 Feb 2011 20:55:43 +0000 SOLiDSequencing AGBT Scores R tight 4 Triathlon - points R high tonight so U could come back & steal the lead!!! BE THERE: Fri. 5-9pm Suite 1106!
Fri, 04 Feb 2011 20:50:52 +0000 apfejes AGBT Tweetup @4pm in poster room by computers - I'll be 10 minutes late for Ion Torrent Talk, but hope to see everyone there.
Fri, 04 Feb 2011 20:41:03 +0000 bioitworld AGBT Moore's Law, what Law? David Bentley: illumina HiSeq2000 exceeding 1 TERABASE sequence/run (up from 200 Gb launch spec 12 months ago).
Fri, 04 Feb 2011 20:39:04 +0000 drjonboyg AGBT This sure beats being at work. Wait a minute, this *is* work!
Fri, 04 Feb 2011 20:32:03 +0000 apfejes AGBT Notes on Tim Yu's talk on autism:
Fri, 04 Feb 2011 20:25:32 +0000 SOLiDSequencing AGBT @iontorrent Workshop NOW: Fri. 3:30-4:00 pm in ISLAND BALLROOM, Chad Nusbaum of Broad Inst.
Fri, 04 Feb 2011 20:22:57 +0000 delahar 1000g,Illumina?,AGBT By my count 90% of the sequence has been done by Is there a viable challenger?
Fri, 04 Feb 2011 20:22:01 +0000 omespeak AGBT Anyone knows if Oxford Nanopore is presenting anything at their suite?
Fri, 04 Feb 2011 20:14:35 +0000 apfejes AGBT @deannachurch Fantastic - we may all be a bit late, if talks run over.
Fri, 04 Feb 2011 20:12:18 +0000 omespeak AGBT No autism gene but genes; WGS + linkage analysis should help in identifying such heterogeneous diseases. - Tim Yu
Fri, 04 Feb 2011 20:11:43 +0000 djschlesinger AGBT @girlscientist Yes, but does that itself mean? Seems rather ambiguous. How can you do association studies without a clear phenotype?
Fri, 04 Feb 2011 20:11:34 +0000 girlscientist AGBT Are there other fields which use the term "bake-off" as much as genomics?
Fri, 04 Feb 2011 20:10:04 +0000 Awesomics genome,sequencing #AGBT update from @gw_dailyscan:
Fri, 04 Feb 2011 20:09:34 +0000 SEQanswers AGBT TimYu: Two great examples of disorders presenting as autism, revealed as something else by WGS by @CompleteGenomic
Fri, 04 Feb 2011 20:08:08 +0000 girlscientist AGBT @djschlesinger he clarified that they use "the autisms" as there are many different spectra under one umbrella.
Fri, 04 Feb 2011 20:03:02 +0000 finchtalk #AGBT Tim Yu. Nice picture, each complete genomics sequence eliminates an excursion into the weeds of open source tools.
Fri, 04 Feb 2011 19:56:53 +0000 djschlesinger AGBT Tim Yu discussing genetics of Autism Spectral disorders. Maybe I missed it, but was Autism defined?
Fri, 04 Feb 2011 19:48:35 +0000 finchtalk #AGBT illumina talk. The spectrum of sequencing technology. Nice representation of throughput, turn around time, instruments. The future
Fri, 04 Feb 2011 19:47:22 +0000 apfejes AGBT. Bloggable notes on David Bently's talk (Illumina)
Fri, 04 Feb 2011 19:46:11 +0000 Copenhagenomics AGBT Thanks to @rforsberg for the mention of our non-profit genomics conference in at - appreciate it! :-)
Fri, 04 Feb 2011 19:39:12 +0000 KamounLab espresso.,AGBT Thank you @CompleteGenomic for the Was much needed!
Fri, 04 Feb 2011 19:37:55 +0000 girlscientist AGBT @SEQanswers just barely! ;)
Fri, 04 Feb 2011 19:35:36 +0000 SEQanswers AGBT @girlscientist At least it's cheaper than 6 million dollars...
Fri, 04 Feb 2011 19:31:56 +0000 djschlesinger AGBT I want a MiSeq!!
Fri, 04 Feb 2011 19:31:27 +0000 girlscientist AGBT David Bentley of Illumina: we have made sequencing better, stronger, faster. [I paraphrase but you get the gist.]
Fri, 04 Feb 2011 19:27:57 +0000 djschlesinger AGBT David Bentley from Illumina discussing clinical sequencing. Tweeting OK sans patient data
Fri, 04 Feb 2011 19:26:51 +0000 SEQanswers AGBT @djschlesinger 12 channel pippin prep in development....!!
Fri, 04 Feb 2011 19:24:06 +0000 apfejes AGBT. @SEQanswers Ironic that the vendors have the most sane twittering policy... or perhaps not.
Fri, 04 Feb 2011 19:22:44 +0000 girlscientist AGBT MT @apfejes: Tweetup (to discuss policy): 4pm, Poster Room in the corner with the computers by the door. Hope to see you there!
Fri, 04 Feb 2011 19:22:39 +0000 djschlesinger AGBT¬タン Just wish it could run more than 4 samples, 12 would be nice: ¬タワ@SEQanswers: Pippin prep 10kb automated gel isolation in 1.5h. Want.
Fri, 04 Feb 2011 19:20:43 +0000 SEQanswers AGBT Pippin prep 10kb automated gel isolation in 1.5h. Want.
Fri, 04 Feb 2011 19:17:34 +0000 djschlesinger AGBT¬タン Touchᅢᄅ: ¬タワ@SEQanswers: Everyone gushing onafternoon tweeting policy: It's a commercial session! ;)
Fri, 04 Feb 2011 19:16:17 +0000 SEQanswers AGBT Everyone gushing onafternoon tweeting policy: It's a commercial session! ;)
Fri, 04 Feb 2011 19:15:50 +0000 apfejes AGBT Tweetup: 4pm, Poster Room in the corner with the computers by the door. Hope to see you there!
Fri, 04 Feb 2011 19:15:16 +0000 trutane genome,sequencing #AGBT update from @gw_dailyscan:
Fri, 04 Feb 2011 19:14:37 +0000 apfejes doingitright,AGBT Impressed with granularity in tweeting policy in afternoon sessions: don't tweet patient data when discussed.
Fri, 04 Feb 2011 19:14:12 +0000 girlscientist AGBT @apfejes tweetups seem to work best when you name a very specific place. First night's was bust bc reception was too big.
Fri, 04 Feb 2011 19:13:22 +0000 djschlesinger AGBT Chris Boles from Sage showing off the Pippin Prep for automated size selection for NGS library prep
Fri, 04 Feb 2011 19:11:04 +0000 omespeak AGBT Slightly improved tweeting policy for this session: free to blog/tweet except for where patient/clinical info is discussed.
Fri, 04 Feb 2011 19:05:56 +0000 SOLiDSequencing AGBT @neilhall_uk You just might - you're currently in the lead: - good luck!
Fri, 04 Feb 2011 19:02:51 +0000 neilhall_uk agbt Stephan Schuster showing very nice ion torrent data....I hope I win one tonight
Fri, 04 Feb 2011 19:02:35 +0000 apfejes AGBT Partial notes on Eric Boerwinkle's talk
Fri, 04 Feb 2011 19:00:12 +0000 apfejes AGBT Anyone intersted in tweetup @4pm, after talks? Would be nice to present unified feedback to conference organizers.
Fri, 04 Feb 2011 18:54:59 +0000 finchtalk #AGBT Steven Schuster. Helico bacter, is a genome from hell. Doing pilots on ion torrent.
Fri, 04 Feb 2011 18:53:56 +0000 SOLiDSequencing AGBT @iontorrent Workshop Fri. 3:30-4:00 pm ISLAND BALLROOM, Chad Nusbaum of Broad Inst.
Fri, 04 Feb 2011 18:49:43 +0000 SEQanswers AGBT,caffeinated @lukejostins with 12.5 hours of talks per day...they are essential
Fri, 04 Feb 2011 18:44:29 +0000 SageScience1 Sage Science Workshop 2:00pm Island Ballroom. Whats new with the Pippin Prep? Come check it out!#AGBT
Fri, 04 Feb 2011 18:42:24 +0000 lukejostins #AGBT must be pretty hectic for both @NEBiolabs and @CompleteGenomic to both decide "pick-me-ups" are the big sell
Fri, 04 Feb 2011 18:39:23 +0000 obahcall AGBT C Bustamante: Differences in ancestry switching between individuals, likely related to diffs in demographic history of MEX and ASW.
Fri, 04 Feb 2011 18:33:58 +0000 SOLiDSequencing AGBT #FF @LifeCorporation @SOLiDSequencing @iontorrent @Grand_Challenge
Fri, 04 Feb 2011 18:33:41 +0000 obahcall AGBT Carlos Bustamante: Importance studying transethnic populations, discusses sequencing of genome of 2 individs, AA and MEX ancestry
Fri, 04 Feb 2011 18:28:46 +0000 SOLiDSequencing PGM,AGBT You can still enter @LifeCorporation Triathlon & play to win @iontorrent sequencer:
Fri, 04 Feb 2011 18:25:17 +0000 SOLiDSequencing AGBT For @LifeCorporation events, visit from your mobile device.
Fri, 04 Feb 2011 18:22:00 +0000 SEQanswers AGBT Bustamente is a great enthusiastic speaker. Think Jack Black does worldwide admixture pop gen
Fri, 04 Feb 2011 18:20:16 +0000 Mikegenome agbt Na18507 na19240 na12878 used in Bustamante analysis of novel variants
Fri, 04 Feb 2011 18:08:12 +0000 sdcrosby AGBT On behalf of those of us still in the cold, thank you so much to all you tweeters!!
Fri, 04 Feb 2011 18:06:20 +0000 finchtalk #agbt life tech lunch. Interesting how short the life cycles are for sequencing instruments.
Fri, 04 Feb 2011 17:46:42 +0000 kmjones96 #AGBT
Fri, 04 Feb 2011 17:43:38 +0000 ChaunceyGrattan agbt How are samples labeled for BioNanomatrix NanoAnalyzer analysis?
Fri, 04 Feb 2011 17:40:05 +0000 SOLiDSequencing PGM #AGBT @LifeCorporation Triathlon Scores - LEADER in contest to win @iontorrent sequencer is...
Fri, 04 Feb 2011 17:37:58 +0000 SOLiDSequencing AGBT @LifeCorporation Lunch/Workshop Now 12-2 pm PALM ROOM: Sequencing Gets Personal. 5 Amazing Speakers - don't miss it!
Fri, 04 Feb 2011 17:00:40 +0000 KamounLab AGBT Primer Extension Capture (PEC) used to enrich 40K-fold heavily degraded Neanderthal mtDNA
Fri, 04 Feb 2011 16:57:38 +0000 girlscientist AGBT Much of Richard Green talk on Neandertals so far has been published. Still interesting but less tweetable.
Fri, 04 Feb 2011 16:56:58 +0000 drjonboyg AGBT This makes a good companion piece to the current talk on extinct hominid genomes:
Fri, 04 Feb 2011 16:55:01 +0000 finchtalk #AGBT RG. majority of sequences from neaderthal bone (~83%) match nothing in the DBs, others microbes, but get enough to seq the genome
Fri, 04 Feb 2011 16:53:31 +0000 owen_w agbt @deannachurch Thanks I'm sure a copacetic policy can get put together.
Fri, 04 Feb 2011 16:52:46 +0000 obahcall AGBT E Boerwinkle: Progressing from GWAS to medical resequencing to experimental systems to clinical epidemiology, with egs from ERIC.
Fri, 04 Feb 2011 16:47:45 +0000 SEQanswers AGBT Gout effect SNP rs2231142 (in urate transporter ABCG2) is in 23andMe. Just checked cool
Fri, 04 Feb 2011 16:47:12 +0000 finchtalk #AGBT Richard Green, evolution from extinct hominids. What can we learn from the dead?
Fri, 04 Feb 2011 16:45:23 +0000 djschlesinger AGBT Richard Green (UCSC) up next. No stated Tweeting policy, however from UC, so probably open to Tweeting.
Fri, 04 Feb 2011 16:43:09 +0000 genomicslawyer AGBT, At @GenomeQuest announces clinical diagnostic/analysis platform for whole-genomes/exomes:
Fri, 04 Feb 2011 16:42:41 +0000 KamounLab AGBT "Waiting for the (#Genomic) Revolution" in Science this week /via @EricTopol @GenomeScience
Fri, 04 Feb 2011 16:42:19 +0000 deannachurch AGBT @owen_w Message heard and I will bring this up with the other members of the committee.
Fri, 04 Feb 2011 16:40:07 +0000 girlscientist AGBT E Boerwinkle: "gout is the Rodney Dangerfield of diseases."
Fri, 04 Feb 2011 16:36:11 +0000 apfejes AGBT Counterpoint, but not really differnt MT @owen_w: commentary on blogging policy.
Fri, 04 Feb 2011 16:31:14 +0000 larry_parnell AGBT Thanks to all Bloggers/Tweeps! Please keep discussing great work of those who allow & ignoring those who wish 2 stay w/in 4 walls
Fri, 04 Feb 2011 16:26:52 +0000 owen_w #agbt My commentary on the blogging policy.
Fri, 04 Feb 2011 16:17:37 +0000 seqcentral #agbt folks: any chance of you all having an "informal formal" discussion on tweeting/blogging policy for *future* conferences?
Fri, 04 Feb 2011 16:17:15 +0000 SEQanswers AGBT Love the GWAS summarizing figure @ , but colors in legend make Tufte shiver
Fri, 04 Feb 2011 16:13:43 +0000 drjonboyg AGBT @Comprendia @mndoci it's at the speakers' discretion.
Fri, 04 Feb 2011 16:11:56 +0000 Comprendia agbt What's the latest on social media policy? @mndoci
Fri, 04 Feb 2011 16:11:06 +0000 NEBiolabs #AGBT attendees: Need a pick-me-up? Check inside your NEBNext cup for a free coupon to pick up an iced coffee or other beverage!
Fri, 04 Feb 2011 16:10:53 +0000 djschlesinger AGBT Eric Boerwinkle (UTexas) phoning in his talk and says we can "tweet him to death"
Fri, 04 Feb 2011 15:44:20 +0000 completegenomic agbt If you need a morning pick-me up, espresso is flowing at Complete Genomics suite - Everglades Room
Fri, 04 Feb 2011 15:41:56 +0000 drjonboyg AGBT @apfejes I'm happy to talk about it if you want to find me.
Fri, 04 Feb 2011 15:39:46 +0000 owen_w agbt @apfejes: "List of speakers who don't allow public discussion"
Fri, 04 Feb 2011 15:39:29 +0000 owen_w agbt @apfejes jermdemo quote: "haha great stuff - Fejes' list of untweetable talks"
Fri, 04 Feb 2011 15:35:47 +0000 illuminainfo HiSeq,AGBT Illumina's Expert Session on
Fri, 04 Feb 2011 15:33:06 +0000 completegenomic #AGBT Genome-scale searches for novel autism genes. Dr. Tim Yu, Harvard Medical School, to present today, 2:40-3, Island Ballroom.
Fri, 04 Feb 2011 15:32:52 +0000 drjonboyg AGBT @apfejes that's illegal now thanks to GINA:
Fri, 04 Feb 2011 15:31:18 +0000 apfejes AGBT. @owen_w The point wasn't to embarass the speakers - most probably don't even know what it means. Those are the holes in my notes.
Fri, 04 Feb 2011 15:26:47 +0000 owen_w agbt embarrassing speakers who dont want 2b blogged is asinine - the _organizers_ failed to prep the speakers before the meeting.
Fri, 04 Feb 2011 15:26:34 +0000 omespeak AGBT Great discussion on twitter about new-born sequencing/genomics in response to last talk. Esp follow @drjonboyg & @djschlesinger
Fri, 04 Feb 2011 15:25:55 +0000 drjonboyg AGBT @apfejes good post, but in the US, newborn screening is universal and paid for by the states, not the patients.
Fri, 04 Feb 2011 15:25:44 +0000 SEQanswers AGBT @drjonboyg Sure, more phys/patient education is a requirement. Just don't like the throw-up-hands-and-hide-info strategy.
Fri, 04 Feb 2011 15:25:29 +0000 UK_Biomek fridayreads,AGBT. and my is the stream of info coming from All sounds very interesting, wish I was there.
Fri, 04 Feb 2011 15:24:44 +0000 raindancetech #AGBT Visit w/ RainDance in Lanai to learn more about our microdroplet-based platform & the new DeepSeq FFPE app.
Fri, 04 Feb 2011 15:22:16 +0000 drjonboyg AGBT @SEQanswers there needs to be a huge improvement in physician understanding of genomics before that happens.
Fri, 04 Feb 2011 15:21:42 +0000 jermdemo AGBT haha great stuff - Fejes' list of untweetable talks: (via @apfejes)
Fri, 04 Feb 2011 15:20:12 +0000 SEQanswers AGBT Not worried about incidentalome. Much like you get conf intervals/ranges on your blood tests...WGS will be presented similarly
Fri, 04 Feb 2011 15:19:58 +0000 drjonboyg AGBT Final note on NBS and genomics: not only is it a fascinating topic, it generates awesome posters
Fri, 04 Feb 2011 15:19:17 +0000 digitalbio AGBT @mndoci According to @finchtalk there were extenuating circumstances at from weather-related travel challenges
Fri, 04 Feb 2011 15:17:40 +0000 Lyro20 AGBT¬タン #Norseqcenter ¬タワ@djschlesinger: Won't the "Incidentalome" prohibit WGS of newborns, or anyone, in a clinical setting?
Fri, 04 Feb 2011 15:14:34 +0000 deannachurch AGBT Martin Hibbard from GIS: No tweeting. I guess we'll just keep discussing that last talk- which was great!
Fri, 04 Feb 2011 15:14:21 +0000 drjonboyg AGBT @djschlesinger the US has 4+ million births a year, more than half under medicaid. Stratified access and disparity is a problem
Fri, 04 Feb 2011 15:13:31 +0000 apfejes AGBT List of speakers who don't allow public discussion @ keeps growing:
Fri, 04 Feb 2011 15:13:13 +0000 omespeak AGBT Liked how Ellen W Clayton referred to Infinite Jest and GATTACA in her talk.
Fri, 04 Feb 2011 15:12:53 +0000 drjonboyg AGBT @djschlesinger right, but there's a difference between individuals and public health, and newborn screening is public health.
Fri, 04 Feb 2011 15:12:42 +0000 SEQanswers AGBT Unfortunate that ChadN had to stop the discussion re: information sharing. Was just getting interesting.
Fri, 04 Feb 2011 15:11:54 +0000 omespeak AGBT Ellen Wright Clayton's talk was informative, entertaining and thought provoking. Also thanks to her for allowing tweeting/blogging.
Fri, 04 Feb 2011 15:11:48 +0000 obahcall AGBT Clayton: Evidence and policy based use is the key to surfing the tsunami of whole genome sequencing.
Fri, 04 Feb 2011 15:11:40 +0000 drjonboyg AGBT We raise some of these issues in this paper: (You can tell this is a policy area I work on and care about)
Fri, 04 Feb 2011 15:10:11 +0000 omespeak AGBT +then should we share the information with patients. However, we may not have a choice, considering patients may demand it.
Fri, 04 Feb 2011 15:09:06 +0000 omespeak AGBT Summary: there will be huge amount of genomic information soon, but do we know what that information means? And if we don't know that+
Fri, 04 Feb 2011 15:08:38 +0000 rhodesmd #AGBT Ellen Clayton gave a talk on ethics of medicine when we have sequence argued against giving out all info brave talk to this audience
Fri, 04 Feb 2011 15:08:36 +0000 obahcall Ellen Wright Clayton: Surfing tsunami of whole genome sequencing, need for developing a policy consensus for access and use of results.#AGBT
Fri, 04 Feb 2011 15:08:14 +0000 djschlesinger AGBT If you can't prevent parents requesting (& getting) antibiotics for their kid's viral ear infection, how will you hold back WGS data?
Fri, 04 Feb 2011 15:07:40 +0000 drjonboyg AGBT Without saying too much, I'm confident that we'll see a lot of research into all of these questions and issues quite soon.
Fri, 04 Feb 2011 15:06:33 +0000 apfejes AGBT: Notes from Ellen Wright Clayton on dangers of human genomic information.
Fri, 04 Feb 2011 15:05:51 +0000 SEQanswers AGBT This is a fantastic talk re:"Incidentalome". Undercurrent of overwhelmed paternalistic pessimism.
Fri, 04 Feb 2011 15:05:13 +0000 omespeak AGBT We have to be rigorous about science and policy to make best use of the upcoming data deluge. Otherwise we will drown: Ellen W Clayton
Fri, 04 Feb 2011 15:04:33 +0000 drjonboyg AGBT In my experience, many in the NBS world are currently really dismissive of WGS unfortunately. we need time to change attitudes
Fri, 04 Feb 2011 15:04:24 +0000 dwmohr AGBT Meant several good arguments FOR limiting patient access to WGS
Fri, 04 Feb 2011 15:03:49 +0000 dsexton_2 #agbt how much protection will governments give?
Fri, 04 Feb 2011 15:02:49 +0000 dwmohr AGBT If tweet policy is any indication, limiting access to WGS will be a hard sell. Several good arguments against it, however
Fri, 04 Feb 2011 15:02:49 +0000 omespeak AGBT Scientific analysis of impact of genetic variation needs to proceed at fast pace for good policy - Ellen W Clayton.
Fri, 04 Feb 2011 15:01:14 +0000 drjonboyg AGBT @djschlesinger great question. I hope so, but tbh don't feel comfortable predicting. So many things have to align (tech, ELSI, budget)
Fri, 04 Feb 2011 15:00:15 +0000 djschlesinger AGBT Ellen: Physicians can't transform SNP data into clinically actionable results.
Fri, 04 Feb 2011 14:59:47 +0000 omespeak AGBT Clayton: Perhaps most controversial - since genetic information *will be* available, patient's desire for info could play minor role.
Fri, 04 Feb 2011 14:59:28 +0000 SEQanswers AGBT "What the patient WANTS will play a minor role" (in genetic information sharing)
Fri, 04 Feb 2011 14:59:03 +0000 drjonboyg AGBT One more thing: there's a difference between individuals sequencing their newborns, and population-level public health NBSeq
Fri, 04 Feb 2011 14:58:03 +0000 djschlesinger AGBT 10+ yrs away? @drjonboyg....I want to see newborn WGS happen population-wide, but there's a LOT that needs to happen first.
Fri, 04 Feb 2011 14:55:37 +0000 omespeak AGBT Clayton: Disclosure of all (genomic) information threatens to sweep away the health-care system
Fri, 04 Feb 2011 14:55:34 +0000 drjonboyg AGBT Don't get me wrong, I want to see newborn WGS happen population-wide, but there's a LOT that needs to happen first.
Fri, 04 Feb 2011 14:54:31 +0000 omespeak AGBT Clayton: Bad science is a problem. Even if we know everything about genome, we cannot predict all disease like they mention in GATTACA
Fri, 04 Feb 2011 14:54:24 +0000 drjonboyg AGBT @djschlesinger certainly something that needs to be worked out. Also, how do you get meaningful informed consent for WGS in 15 min?
Fri, 04 Feb 2011 14:53:24 +0000 djschlesinger AGBT Absolutely! @drjonboyg: Also, clinical WGS needs to get error rates down by three or more orders of magnitude for NBS
Fri, 04 Feb 2011 14:52:15 +0000 omespeak AGBT Clayton: As we look at genomic testing, vast majority of findings will have pleiotropic affects.
Fri, 04 Feb 2011 14:51:49 +0000 drjonboyg AGBT Also, clinical WGS needs to get error rates down by three or more orders of magnitude for NBS
Fri, 04 Feb 2011 14:49:55 +0000 omespeak AGBT Ellen Wright Clayton: debate on incidental findings - how much information do you give back?
Fri, 04 Feb 2011 14:49:40 +0000 drjonboyg AGBT As an example, Illinois balked at deploying a new method of NBS because it would have cost $5 million to conduct the pilot.
Fri, 04 Feb 2011 14:48:36 +0000 djschlesinger AGBT Won't the "Incidentalome" prohibit WGS of newborns, or anyone, in a clinical setting?
Fri, 04 Feb 2011 14:47:55 +0000 drjonboyg AGBT Not sure I agree that we're going to have routine newborn WGS until the costs come down to $200 or less, the States can't afford it.
Fri, 04 Feb 2011 14:46:14 +0000 SEQanswers AGBT Ellen Clayton: In a few years, newborns will be sequenced when they can't get away.
Fri, 04 Feb 2011 14:44:45 +0000 omespeak AGBT Ellen Wright trying to make a case that complete disclosure WGS data could lead to disaster.
Fri, 04 Feb 2011 14:44:37 +0000 dsexton_2 #agbt Ellen is an expert in the bioethics around sequencing
Fri, 04 Feb 2011 14:44:04 +0000 djschlesinger Ellen Wright Clayton (Vanderbilt) wants to "stir things up". Tweet away......#AGBT
Fri, 04 Feb 2011 14:35:33 +0000 KapaBiosystems AGBT Come visit our poster to see latest improvement to NGS sample prep workflow.
Fri, 04 Feb 2011 14:35:10 +0000 KapaBiosystems AGBT Library quantification kit compatible for Ion Torrent instrument. Library quant. kits available for all current NGS platforms.
Fri, 04 Feb 2011 14:25:30 +0000 neilhall_uk agbt this is all published work..why cant we tweet.?
Fri, 04 Feb 2011 14:24:29 +0000 MaliciaRogue AGBT . ¬ルᄏ @genomeresearch: 60 Complete, High-Coverage Human Genomes -- for Study by the Global Research Community...
Fri, 04 Feb 2011 14:10:45 +0000 wyattsgirl AGBT Following the Tweets... wish more folks could give more info to those waitlisted... ha! dang forbidders of the tweet!
Fri, 04 Feb 2011 14:09:06 +0000 deannachurch AGBT Jim Lupski up first thing this AM. No tweets b/c he is talking about patient data.
Fri, 04 Feb 2011 14:07:12 +0000 djschlesinger AGBT Dr. Lupski up first, Tweeting prohibited due to the inclusion of patient data.
Fri, 04 Feb 2011 13:46:59 +0000 BioAcousticGal slow,agbt Sounds like we missed a good one! @neilhall_uk start this morning due to the lifetech party last night...ouch!
Fri, 04 Feb 2011 13:26:29 +0000 neilhall_uk agbt #slow start this morning due to the lifetech party last night...ouch!
Fri, 04 Feb 2011 12:51:39 +0000 completegenomic #AGBT Customer case studies to be presented in Everglades Room today: 10:35-10:50, 1:30-1:45, 5-5:15. Still need an iPad? - drawing @ 6!
Fri, 04 Feb 2011 12:24:04 +0000 raindancetech AGBT Join us @ our workshop today @ 2pm to learn about Ultra-Deep Sequencing & Methylation Analysis of FFPE Tumor Samples w/ Microdroplets
Fri, 04 Feb 2011 12:19:19 +0000 illuminainfo AGBT Illumina will be at the Bronze Sponsors workshop today at 2:00 p.m. Island Ballroom
Fri, 04 Feb 2011 12:18:32 +0000 mndoci AGBT Strata videos go live a day after talks, has a default no blogging policy. Something in the world of science is just not right
Fri, 04 Feb 2011 11:42:14 +0000 pjacock AGBT Galaxy 2011 Community Conference, May 25-26, Lunteren, The Netherlands
Fri, 04 Feb 2011 06:49:48 +0000 bffo AGBT, Great PB user group evening, as well as good LT soiree sorry I missed the tweetup, maybe tomorrow evening?
Fri, 04 Feb 2011 06:02:20 +0000 SOLiDSequencing AGBT Stay Fresh & Focused During Yoga w/ @iontorrent every morning Capri 2 & 3, 7:00 - 8:00 AM
Fri, 04 Feb 2011 05:43:03 +0000 SOLiDSequencing AGBT Fri. @LifeCorporation Lunch/Workshop 12-2 pm PALM ROOM: Sequencing Gets Personal. 5 amazing speakers - don't miss it!
Fri, 04 Feb 2011 05:37:54 +0000 SOLiDSequencing AGBT,PGM @LifeCorporation Triathlon Scores just in! Does Baylor keep lead in competition for @iontorrent sequencer...???
Fri, 04 Feb 2011 04:44:25 +0000 abhishekpratap AGBT 60 Complete, High-Coverage Human Genomes -- for Study by the Global Research Community -- By Complete Genomics :
Fri, 04 Feb 2011 04:42:49 +0000 girlscientist AGBT, If you lose AT&T service on your iPhone here at go to settings then restore network settings. Thanks Shawn Levy for tip!
Fri, 04 Feb 2011 04:04:54 +0000 omespeak AGBT Any other tweeps at the All Night Long party?
Fri, 04 Feb 2011 02:59:08 +0000 infoecho tweetleak,AGBT It seems that we need a for
Fri, 04 Feb 2011 02:24:51 +0000 apfejes AGBT A big thank you and round of aplause for the speakers who allowed twittering/blogging today!
Fri, 04 Feb 2011 02:22:19 +0000 KamounLab AGBT Watch bionanomatrix movie "400 kb DNA entering nanochannel"
Fri, 04 Feb 2011 02:10:34 +0000 apfejes AGBT Notes on Maria Mendez-Lago, BC Cancer:
Fri, 04 Feb 2011 02:09:56 +0000 rafalwoycicki PAG,AGBT I have just forgotten Who can help me? What animal genome announced at was done with optical mapping by @OpGen & @BGI_events ? ?
Fri, 04 Feb 2011 02:03:59 +0000 djschlesinger AGBT Was BioNanomatrix the star this year?
Fri, 04 Feb 2011 02:03:14 +0000 KamounLab AGBT Link to Brian Haas Trinity package for RNA-Seq de novo assembly [coming soon]
Fri, 04 Feb 2011 01:48:13 +0000 drjonboyg AGBT This session has been the highlight of so far. Probably because I'm a total geek.
Fri, 04 Feb 2011 01:47:34 +0000 drjonboyg AGBT Anyone else think these nanochannels look like the matrix?
Fri, 04 Feb 2011 01:45:23 +0000 girlscientist AGBT Kerstin Lindblad-Toh asked me to pass on link to new Science for Life Lab being formed in Uppsala:
Fri, 04 Feb 2011 01:43:50 +0000 djschlesinger AGBT Han Cao from BioNanomatrix showed a cool movie of 400kb DNA fragment traveling through a nanochannel.
Fri, 04 Feb 2011 01:39:34 +0000 SOLiDSequencing AGBT.,PGM @LifeCorporation Triathlon tonight Who gets closer to winning an @iontorrent sequencer?
Fri, 04 Feb 2011 01:33:47 +0000 apfejes AGBT No blogging on Michelle Sam's talk.
Fri, 04 Feb 2011 01:30:51 +0000 apfejes AGBT Notes on Lara Bull-Otterson's talk on finding viruses in unmapped reads for cancer.
Fri, 04 Feb 2011 01:28:59 +0000 deannachurch AGBT JO: solid state nanopore, hyb a probe and measure probe loc. //concept
Fri, 04 Feb 2011 01:28:17 +0000 girlscientist AGBT The Apple haters are winning: AT&T no service specifically for our iPhones/iPads. Can anyone explain it?
Fri, 04 Feb 2011 01:26:49 +0000 djschlesinger AGBT Solid state versus protein nanopores. which do you chose?
Fri, 04 Feb 2011 01:26:00 +0000 djschlesinger AGBT @SEQanswers likely true, but probably not enough. Point is kind of moot because the threat of bioterrorism is over stated.
Fri, 04 Feb 2011 01:24:21 +0000 SOLiDSequencing AGBT Somehow escaped it thus far? Zheng Lab, Lady Gaga Parody / Science Grad School "Bad Project"
Fri, 04 Feb 2011 01:23:31 +0000 deannachurch agbt JO: Not a bioinformatics problem, not enough info content in current reads to get the right answer at all length scales.
Fri, 04 Feb 2011 01:22:32 +0000 SEQanswers AGBT @djschlesinger I agree, but you heard her mention her database...which is prob stuffed with all examples of relevant biothreat bugs
Fri, 04 Feb 2011 01:20:42 +0000 djschlesinger AGBT @SEQanswers microbial genomes are littered w/ mobile element. task is impossible, unless you link it to a modification already publish
Fri, 04 Feb 2011 01:18:58 +0000 deannachurch agbt John Oliver from NABsys on chr lenght contigs. Tweet friendly
Fri, 04 Feb 2011 01:18:05 +0000 omespeak AGBT Ironically it was a speaker from US army who was ok with tweeting/blogging.
Fri, 04 Feb 2011 01:14:12 +0000 SEQanswers AGBT,thearmyisscary @djschlesinger Probably looking for some combination of mobile elements, pieces of vectors, or novel junctions.
Fri, 04 Feb 2011 01:13:35 +0000 omespeak AGBT Lauren McNew from US military's Chemical Bio Centre - 'if you can put a sequencing machine to a camel we will buy it'
Fri, 04 Feb 2011 01:13:22 +0000 deannachurch AGBT LM: looking for a field seq unit, preferably in camo.
Fri, 04 Feb 2011 01:12:44 +0000 apfejes AGBT Notes from Obi Grifith's talk on molecular predictors for drug response:
Fri, 04 Feb 2011 01:12:12 +0000 djschlesinger AGBT How do you tell if a microbial genome has been "engineered"?
Fri, 04 Feb 2011 01:05:35 +0000 djschlesinger AGBT Lauren McNew from ECBC can sequence a microbial genome in 36 hours!
Fri, 04 Feb 2011 01:05:18 +0000 girlscientist AGBT Obi Griffith on cancer genomics: RNAseq analysis for breast cancer subtypes.
Fri, 04 Feb 2011 01:03:16 +0000 rforsberg agbt McNew talk; finally a lab that can handle both genomics and explosives
Fri, 04 Feb 2011 01:02:25 +0000 deannachurch AGBT LM: exercises to plan for identifying pathogens in case of a biothreat, using 454.
Fri, 04 Feb 2011 01:00:27 +0000 deannachurch AGBT Laura McNew tech session. Threat analysis- cool sounding!
Fri, 04 Feb 2011 00:58:00 +0000 drjonboyg AGBT A particularly cool talk on a novel nanopore for sequencing that I can't tell you about.
Fri, 04 Feb 2011 00:38:32 +0000 djschlesinger AGBT @omespeak not so much product placement, but it's patronizing pop-culture tone. While cool, it wasn't suitable for the audience.
Fri, 04 Feb 2011 00:38:15 +0000 omespeak AGBT At the Technology session: talk about nanopores. No tweeting allowed :(
Fri, 04 Feb 2011 00:37:56 +0000 suganthibala AGBT MT @girlscientist Freudian slip? Salzberg means to say he'll give us cursory description of Bowtie, instead says "curse." You decide.
Fri, 04 Feb 2011 00:37:03 +0000 rforsberg AGBT As of this year, Europe will also have a genomics conference inspired by AGBT. It is called Copenhagenomics -
Fri, 04 Feb 2011 00:36:22 +0000 omespeak AGBT Will talk about the movie and PacBio in details later. Some people seem pissed about the product placement.
Fri, 04 Feb 2011 00:35:47 +0000 SEQanswers AGBT Genomic Technology Session = Full. Tweets = Empty by request of speaker.
Fri, 04 Feb 2011 00:35:22 +0000 neilhall_uk agbt Well done to James hayfield for getting in a question on how to end world hunger at the pacbio dinner
Fri, 04 Feb 2011 00:34:38 +0000 omespeak agbt Couldn't Tweet from the Pac Bio dinner & movie. But movie was an interesting documentary about 'new biology' (mostly systems).
Fri, 04 Feb 2011 00:30:18 +0000 apfejes AGBT One more speaker who can't be blogged: Olivier Harismendy.
Fri, 04 Feb 2011 00:29:46 +0000 JoPet39 Not that dinner and a movie wasn't captivating, but coffee should flow freely when evening sessions are scheduled.#AGBT
Fri, 04 Feb 2011 00:29:34 +0000 SOLiDSequencing SOLiD,sequencing,AGBT Stop by Suites 1104-1106 for @LifeCorporation Triathlon and to see + @iontorrent instruments.
Fri, 04 Feb 2011 00:24:50 +0000 nanopore AGBT Jens Gundlach up now on nanopore research in the Island Ballroom
Fri, 04 Feb 2011 00:15:37 +0000 rdeborja AGBT, At the cancer genomics talks at my F-Cancer t-shirt was a huge hit. @letsfcancer, @msfuckcancer
Fri, 04 Feb 2011 00:02:06 +0000 drjonboyg AGBT Explain to me how my blackberry can have an AT&T signal (edge) when neither my iPhone or iPad have one?
Thu, 03 Feb 2011 23:43:55 +0000 SOLiDSequencing AGBT @LifeCorporation Triathlon: Stage 1 REPEAT: 7-11pm Suite 1104, Stage 2: 7-11pm Suite 1105.
Thu, 03 Feb 2011 23:40:53 +0000 SOLiDSequencing #AGBT @LifeCorporation Triathlon, chance to win an @iontorrent PGM sequencer:
Thu, 03 Feb 2011 23:38:29 +0000 rforsberg agbt Would love to see the Monsanto single-corn-chip machine run though. Looked like something out of Brazil, the movie
Thu, 03 Feb 2011 23:36:36 +0000 drjonboyg AGBT Left the PacBio thing before the questions, had a feeling it might have gotten snarky.
Thu, 03 Feb 2011 23:36:06 +0000 rforsberg agbt It seems pretty old fashioned to use "new" biology to select solely for yield in food crops
Thu, 03 Feb 2011 23:28:42 +0000 drjonboyg AGBT Famine only happens when food shortage combines with a government preventing people from moving.
Thu, 03 Feb 2011 23:28:21 +0000 Mikegenome agbt So for a free meal we watched a 30 min PacBio commercial
Thu, 03 Feb 2011 23:27:11 +0000 illuminainfo MiSeq,illuminalounge.,AGBT Meet and greet the instrument at the Fri (2/4): 6-7pm, Sat (2/5): 1-5pm
Thu, 03 Feb 2011 23:24:49 +0000 drjonboyg AGBT Ok, that one I take issue with. Famines are political in nature, they're not going to be solved by GM crops.
Thu, 03 Feb 2011 23:24:11 +0000 djschlesinger AGBT A movie about corn eugenics? @drjonboyg: Actually, this would be a great movie to have shown my science policy class @UK_Patterson.
Thu, 03 Feb 2011 23:21:39 +0000 drjonboyg AGBT Actually, this would be a great movie to have shown my science policy class @UK_Patterson.
Thu, 03 Feb 2011 23:17:33 +0000 drjonboyg AGBT I'll have you all know I'm being incredibly restrained right now. I do like the CGI animations in this movie though.
Thu, 03 Feb 2011 23:15:57 +0000 SOLiDSequencing AGBT. @ChaunceyGrattan You're welcome! We love it, too. Lots of great info at
Thu, 03 Feb 2011 23:11:20 +0000 djschlesinger AGBT True story: @dwmohr: The new biology sounds alot like the old biology. It's the computers that can't keep up
Thu, 03 Feb 2011 23:09:21 +0000 SOLiDSequencing AGBT Accelerate Innovative Solutions: Mike Lelivelt at the @LifeCorporation @Grand_Challenge Workshop
Thu, 03 Feb 2011 23:09:11 +0000 dwmohr AGBT The new biology sounds alot like the old biology. It's the computers that can't keep up
Thu, 03 Feb 2011 23:05:09 +0000 ChaunceyGrattan AGBT this tag is kinda amazing... big shout out to the tweeps keeping me in the loop!
Thu, 03 Feb 2011 22:57:24 +0000 drjonboyg AGBT @dgmacarthur except most of the 'no tweeds allowed' speakers are academics, and most of the data is published or in the process.
Thu, 03 Feb 2011 22:55:30 +0000 dgmacarthur AGBT @drjonboyg Although, to be fair, has a far higher density of commercially sensitive material in presentations.
Thu, 03 Feb 2011 22:54:38 +0000 dgmacarthur AGBT @drjonboyg Sorry to see that attitude of speakers to twitter is so different from, say, BoG (where ~90% of speakers allowed tweets).
Thu, 03 Feb 2011 22:47:29 +0000 drjonboyg AGBT Not having Internet access has saved me from making a lot of sarcastic tweeds. Probably a good thing.
Thu, 03 Feb 2011 22:42:21 +0000 SOLiDSequencing AGBT,PGM High jumper competes in @LifeCorporation Triathlon for chance to win an @iontorrent sequencer.
Thu, 03 Feb 2011 22:35:47 +0000 SOLiDSequencing NGS,AGBT @apfejes Targeted Reseq = 50%+ runs, then RNASeq, ChIPSeq, say JNoonan-Yale, RSteen-Harvard, JMullikin-NIH.
Thu, 03 Feb 2011 22:33:26 +0000 SOLiDSequencing AGBT Player competes in @LifeCorporation Triathlon for chance to win an @iontorrent sequencer.
Thu, 03 Feb 2011 22:29:32 +0000 SOLiDSequencing AGBT. Maneesh Jain opens the @LifeCorporation @Grand_Challenge workshop
Thu, 03 Feb 2011 22:22:08 +0000 djschlesinger AGBT Any Tweeps at the PacBio dinner?
Thu, 03 Feb 2011 22:05:32 +0000 owen_w AGBT @
Thu, 03 Feb 2011 22:03:47 +0000 girlscientist AGBT Awwww look at the kittehs.
Thu, 03 Feb 2011 22:02:38 +0000 KamounLab AGBT @girlscientist @deannachurch @apfejes Cute animal picture show continues. But wait we're not supposed to tweet about it...
Thu, 03 Feb 2011 21:59:00 +0000 NEBiolabs AGBT Check out the posters from New England Biolabs at From sample prep to bacteria making electricity:posters 7,63,92,155,184,199&206
Thu, 03 Feb 2011 21:51:15 +0000 apfejes internet,youredoingitwrong,AGBT This may be the first time in my life I'm being barred from twittering about cute kitten pictures...
Thu, 03 Feb 2011 21:50:56 +0000 deannachurch AGBT This session totally wins for cute animal pictures.
Thu, 03 Feb 2011 21:47:42 +0000 SOLiDSequencing PGM #AGBT Triathlon Scores: It's not too late to take the lead and win an @iontorrent sequencer!
Thu, 03 Feb 2011 21:46:00 +0000 apfejes feb3,AGBT. @paniniVani I proposed we start using the hashtag. :-P
Thu, 03 Feb 2011 21:45:37 +0000 drio AGBT bowtie maps 3% > reads than bwa. What tool has the higher number of correct alignments? What alignments deliver t best SNP calls
Thu, 03 Feb 2011 21:44:57 +0000 apfejes AGBT Has Chip-Seq dissapeared from the map this year? No ChIP-Seq posters, and everyone just glosses over the epigenetics.
Thu, 03 Feb 2011 21:42:28 +0000 dwmohr #AGBT tweeting/blogging drives interest. Isn't that what we're after?
Thu, 03 Feb 2011 21:40:59 +0000 paniniVani AGBT @apfejes When did become Egypt? (via @ronald_duncan)
Thu, 03 Feb 2011 21:40:36 +0000 rafalwoycicki AGBT @omespeak sample prep is crucial
Thu, 03 Feb 2011 21:38:45 +0000 paniniVani AGBT Salzberg: adding onto TopHat- to look for fusion genes. "coming soon" (via @deannachurch)
Thu, 03 Feb 2011 21:37:12 +0000 owen_w agbt my view: when tweeting is outlawed, only outlaws will tweet.
Thu, 03 Feb 2011 21:37:11 +0000 girlscientist AGBT Tried to get my HudsonAlpha colleague Greg Barsh, to allow tweeting etc., but no success.
Thu, 03 Feb 2011 21:36:17 +0000 deannachurch AGBT Greg Barsh up next- no tweeting.
Thu, 03 Feb 2011 21:33:23 +0000 apfejes AGBT Oops, wrong link - Notes on Steven Salzber's (VERY OPEN) talk:
Thu, 03 Feb 2011 21:31:34 +0000 deannachurch AGBT Salzberg: Getting Bowtie2 requirements during Q&A :)
Thu, 03 Feb 2011 21:30:48 +0000 djschlesinger AGBT Salzberg makes me rethink my career I should have been a bioinformatician.
Thu, 03 Feb 2011 21:27:35 +0000 omespeak AGBT Unlike, last year, no major announcements at , other than @CompleteGenomic's release of 60 human genomes.
Thu, 03 Feb 2011 21:23:09 +0000 SEQanswers AGBT Next package in the Tuxedo suite: Handcuffs. Harrrrrr.
Thu, 03 Feb 2011 21:21:20 +0000 deannachurch AGBT Salzberg: adding onto TopHat- to look for fusion genes. "coming soon"
Thu, 03 Feb 2011 21:21:12 +0000 girlscientist AGBT Salzberg: coming soon to a computer near you is TopHat-Fusion! Special-purpose routines for finding gene fusions in seq data.
Thu, 03 Feb 2011 21:21:04 +0000 neilhall_uk agbt Tophat fusion coming soon for finding fusion genes
Thu, 03 Feb 2011 21:17:37 +0000 rdeborja AGBT Bowtie2 definitely sounds interesting. Finally full support for indels.
Thu, 03 Feb 2011 21:16:54 +0000 neilhall_uk agbt Bowtie2 coming in spring
Thu, 03 Feb 2011 21:16:50 +0000 OoohMySeat AGBT. tweet censoring My view: It takes time for some to get comfortable with the power of twitter. Respect them, they will come around.
Thu, 03 Feb 2011 21:16:11 +0000 djschlesinger AGBT Bowtie 2 available this spring.
Thu, 03 Feb 2011 21:15:37 +0000 deannachurch AGBT- @rafalwoycicki not anti-tweet rules. Speaker opt-in policy. No rules broken.
Thu, 03 Feb 2011 21:15:26 +0000 djschlesinger AGBT Salzberg: Bowtie and BWA don't always map the same reads. ~7% difference.
Thu, 03 Feb 2011 21:15:05 +0000 ronald_duncan AGBT @apfejes When did become Egypt?
Thu, 03 Feb 2011 21:14:48 +0000 neilhall_uk agbt For the non-cs crowd (like me) that was a great explanation of bs transform. Thanks Steven
Thu, 03 Feb 2011 21:14:23 +0000 deannachurch AGBT @girlscientist aligns more reads- I haven't seen a measure of accuracy yet.
Thu, 03 Feb 2011 21:14:16 +0000 rafalwoycicki AGBT Thank to everyone who break the anti-tweet rules at
Thu, 03 Feb 2011 21:13:28 +0000 girlscientist AGBT Salzberg: Bowtie program still faster than SOAP2 and BWA programs for alignments, and is more accurate.
Thu, 03 Feb 2011 21:08:29 +0000 girlscientist AGBT Freudian slip? Salzberg means to say he'll give us cursory description of Bowtie, but instead says "curse." You decide.
Thu, 03 Feb 2011 21:07:03 +0000 omespeak agbt Most impressed by Life Tech's Starlight Quantum dot 'nanosequencing machines'. But have heard the talk by Beecham earlier.
Thu, 03 Feb 2011 21:05:03 +0000 Sequilabs> AGBT Sequilabs: CompleteGenomic: New genomes will be available through our website < and t...
Thu, 03 Feb 2011 21:05:03 +0000 Sequilabs AGBT, Sequilabs: CompleteGenomic: Need a caffeine pick-me up at Expresso in Everglade: CompleteGenomic: Need a ...
Thu, 03 Feb 2011 21:05:03 +0000 Sequilabs AGBT Sequilabs: CompleteGenomic: Interested in our commercial sequencing services? Visit our hospitality suite ...
Thu, 03 Feb 2011 21:04:52 +0000 omespeak AGBT NABSys showed *some* data on nanopore sequencing by hybridization. Still no real sequencing information.
Thu, 03 Feb 2011 21:04:27 +0000 rdeborja AGBT Sitting at Steven Salzberg's High Performance Alignment and Analysis of Next Generation Sequences talk on Bowtie
Thu, 03 Feb 2011 21:04:14 +0000 deannachurch AGBT Salzberg: software discussed in talk.
Thu, 03 Feb 2011 21:03:22 +0000 girlscientist AGBT Salzberg covering three of his assembly programs: Bowtie, Tophat, and Cufflinks. (what's next? Spats? Insert your own joke here.)
Thu, 03 Feb 2011 21:02:18 +0000 girlscientist AGBT Next speaker, Salzberg, says "I'd be delighted if you tweet and blog whatever you'd like about my talk,"
Thu, 03 Feb 2011 21:02:12 +0000 deannachurch AGBT Steve Salzberg: High-Performance Alignment and analysis of NGS. tweetable...
Thu, 03 Feb 2011 21:01:53 +0000 omespeak AGBT Lots of posters at focused on improved sample prep for various platforms. Very few on new sequencing techniques.
Thu, 03 Feb 2011 21:00:12 +0000 girlscientist AGBT Ssecond attempt at tweetup tonight at lobby bar, 9:30pm after night session.
Thu, 03 Feb 2011 20:58:45 +0000 omespeak AGBT General feeling from talking with various people at - sharing of and moving NGS data between various sites will be a huge issue.
Thu, 03 Feb 2011 20:54:54 +0000 apfejes AGBT Some thoughts on talks that are forbidding tweeting/blogging.
Thu, 03 Feb 2011 20:47:48 +0000 a__muse AGBT Looks like is asking people not to tweet. So I guess blogging is also out @omespeak ?
Thu, 03 Feb 2011 20:35:29 +0000 bioscribe AGBT Dinner and a movie tonight @ featuring "The New Biology" documentary by PacBio. Palms Ballroom 5:00 pm.
Thu, 03 Feb 2011 20:22:25 +0000 KamounLab AGBT New genomics Institute at Sweden's Uppsala University modeled on the Broad. Recruiting now.
Thu, 03 Feb 2011 20:20:27 +0000 girlscientist AGBT Kerstin ends with saying new institute modeled on Broad is starting in Uppsala and they are looking for bright young scientists.
Thu, 03 Feb 2011 20:19:34 +0000 apfejes wishuwerehere,AGBT I'm sure this part is Tweetable: inbreeding dogs is bad, cancer is complex in dogs too. The rest is secret. (-:
Thu, 03 Feb 2011 20:17:12 +0000 neilhall_uk agbt It's submitted for publication but we can't tweet it!
Thu, 03 Feb 2011 20:16:11 +0000 rafalwoycicki AGBT,PAG I should be there now at the same was with
Thu, 03 Feb 2011 20:10:25 +0000 raindancetech #AGBT @ 7:30pm Thurs. - UCSD's Oliver Harismendy on analyzing chromosomal 'hot spots' in tumors w/ RainDance's DeepSeq FFPE Solution
Thu, 03 Feb 2011 20:09:00 +0000 SEQanswers AGBT I have canine compulsive disorder to tweet the details about this talk.
Thu, 03 Feb 2011 20:03:24 +0000 Sequilabs> AGBT CompleteGenomic: New genomes will be available through our website < and the Bionimbu...
Thu, 03 Feb 2011 20:03:24 +0000 Sequilabs AGBT, CompleteGenomic: Need a caffeine pick-me up at Expresso in Everglade: CompleteGenomic: Need a caffeine pi...
Thu, 03 Feb 2011 20:03:24 +0000 Sequilabs AGBT CompleteGenomic: Interested in our commercial sequencing services? Visit our hospitality suite in the Ever...
Thu, 03 Feb 2011 20:01:24 +0000 apfejes AGBT Not happy about it, but this is my list of talks for which I'm not allowed to publish my notes:
Thu, 03 Feb 2011 19:59:29 +0000 apfejes topsecret,canine,genome,AGBT Yet another no-tweet... this time on dog genomics.
Thu, 03 Feb 2011 19:59:12 +0000 neilhall_uk agbt. Been looking at the illumina miseq at Very very nice piece of kit. But I almost object to them making sequencing too easy.
Thu, 03 Feb 2011 19:54:57 +0000 SOLiDSequencing cancer.,AGBT New term: chromothripsis: a single catastrophic event leading to chromosomes getting interlinked in
Thu, 03 Feb 2011 19:50:30 +0000 Mikegenome agbt @drjonboyg my iPhone lost signal too. Had it in earlier sessions. Wifi working
Thu, 03 Feb 2011 19:48:42 +0000 Mikegenome agbt Blocked from tweeting what turns out midway through the Wein. talk to be published data... Perhaps the second half is unpublished.
Thu, 03 Feb 2011 19:45:33 +0000 drjonboyg AGBT, Furthering connectivity problems at now I can't get an AT&T signal on my iPad or iPhone. eek.
Thu, 03 Feb 2011 19:44:08 +0000 razZ0r AGBT Follow the hashtag for new stuff on genomes, biotech, genome sequencing, etc. (If the speaker allows tweeting, stupid policy, LOL.)
Thu, 03 Feb 2011 19:43:56 +0000 girlscientist AGBT Weinshilboum cites a recent paper, Nov 2010, in J Clin Oncol so I'd say one should look there if one wants an idea of his talk.
Thu, 03 Feb 2011 19:40:09 +0000 girlscientist AGBT Next talk, Kerstin Lindblad-Toh, not going to be tweetable either.
Thu, 03 Feb 2011 19:34:32 +0000 SEQanswers agbt First talk after poster session: Richard Weinshilboum = no tweets.
Thu, 03 Feb 2011 19:33:11 +0000 apfejes AGBT Gah... no blogging for Richard Weinshiboum. Not sure he knows what twittering is, tho... (joke about issues with the mouse...)
Thu, 03 Feb 2011 19:33:11 +0000 girlscientist AGBT First talk at afternoon session is Richard Weinshilboum, but he's requested no tweeting.
Thu, 03 Feb 2011 19:29:50 +0000 LIFECorporation AGBT, Getting ready for tonight's reception at hope to see you here.
Thu, 03 Feb 2011 19:29:39 +0000 cliffmcc #AGBT is asking people to not tweet during conference talks. Guess they can't take notes either?
Thu, 03 Feb 2011 19:26:18 +0000 LIFECorporation AGBT Tonight's event, will we see you there? @solidsequencing @iontorrent