Up at 5AM: The 5AM Solutions Blog

Advances in Genome Biology and Technology Conference 2010

Posted on Sat, Feb 27, 2010 @ 01:04 PM

I'm just back from Florida and decompressing from the Advances in Genome Biology and Technology (AGBT) Conference. It takes place every winter (this is the 11th year) on Marco Island, which is somewhat inconveniently located about an hour's drive from the Fort Myers airport. I flew direct from Baltimore but a lot of people had to connect from Charlotte, Chicago and other places.
This is the first time I've attended this meeting, but it reminds me of the Genome Sequencing and Analysis Conferences (GSAC) from 10 or 15 years ago. Those conferences were in Hilton Head, South Carolina, among other places, which was also far from an airport. When the Human Genome Project was getting underway, GSAC was an exciting blend of science and technology with a large vendor presence.
AGBT doesn't have vendor booths like GSAC used to, but there were hospitality suites and a good number of vendor-sponsored 'workshops' which could cynically be called advertisements, but which in most cases were pretty informative.
There's no way for me to cover all the developments in one blog post, but I'll give a few highlights. Illumina maintained its market lead by rolling out a new sequencer, the HiSeq 2000. It's the same basic technology as its earlier Genome Analyzer line, but they can now do good coverage of two human genomes in a single run for $10,000. Roche/454 seems to be getting marginalized and didn't have much of a presence. Helicos was still present with their single-molecule sequencer but appears to marred by high error rates. Life Technologies is also improving its SOLiD platform to increase throughput and is nipping at Illumina's heels. There was no mention at all of the Polonator.
But the new technologies were the ones that dominated the meeting. Life is working on enhancements to the 2-base encoding on the SOLiD platform that they claim will improve accuracy and also stop reporting data in colorspace, which is often confusing. Complete Genomics has delivered on their promise from last year's AGBT to start delivering full human genome sequences, of apparently good quality, from their sequencing factory (they don't sell sequencers, they sell the sequence data).
Pacific Biosciences had a workshop where they talked about their new sequencer. It uses DNA polymerase molecules to incorporate labelled nucleotides on a single DNA molecule, detecting each incorporation to reveal the sequence. They also discussed some neat variations, such as resequencing the same molecule multiple times to get higher quality data, and producing so-called strobed reads, which allow reading sections of longer molecules, giving the same benefit as paired-end reads for spanning repeats and identifying structural variations. Their machine also has the benefits of being able to generate longer reads (up to 10,000bp, but only on some reads in a run) and being able to do runs in hours instead of days. But unlike Complete Genomics and the more established companies, they didn't have any reports from collaborators that used their system, and there were questions about the accuracy of their sequence which didn't really get answered.
But the real fireworks happened in the last two talks of the conference. The first one was from Life Technologies, reporting on a new kind of sequencer they hope to roll out within the next year. This one uses DNA polymerase tethered to a nanoball that emits light in a specific frequency that excites dye-labelled nucleotides as they are incorporated. They had several cool movies to demonstrate the idea. Like Pacific Biosciences, this method promises fast run times and potentially long read lengths. However, in this case the polymerase is free, not in a tiny well, so that once it stops working, it can be replaced with another one. This means the read lengths might not be as unpredictable. It means they can also resequence the same molecule multiple times for higher accuracy. Also, the machine itself is quite small. This is clearly interesting technology but early in the commercialization process.
Lastly, Ion Torrent described their new sequencer, which should be available in the first half of this year. In some ways it is similar the earlier 454 machine, and in fact Ion Torrent's CEO also worked on the 454 machine. Ion Torrent's device is also based on using DNA polymerase but they made a huge deal out of the fact that their device is based on silicon semiconductor technology. They capture the positive charge generated by incorporation of one (or more) nucleotides and convert that to a digital signal on their chip-like device. Their device is small and promises fast run times, but they didn't talk about sequence quality or the sample preparation process. The biggest distinction they made was that they could make the devices very cheap by relying on existing semiconductor fabrication technology and existing factories.
This is by necessity a brief overview, and I hope to post more entries as the community processes all the information from the ABGT meeting and some of these new machines become more widely available. But it was an exciting, inspiring, and somewhat overwhelming meeting. I think the biggest challenges will be to figure out which machines are best for which applications and find good ways to process and understand the huge volumes of data that will be generated.
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Many feet, many paths to EHR

Posted on Sat, Feb 27, 2010 @ 01:03 PM

When Bill Clinton had stents placed in one of his arteries a few weeks ago, our colleague Christine Quern (Feinstein Kean Healthcare) mentioned that she’d heard a physician commentator on the local newscast state that Clinton went to Columbia Presbyterian Hospital for treatment “because that’s where his medical records were.”

I’ll forgive a news commentator for inaccuracy under fire. But in this era of “health IT,” with intense focus and funding for creating electronic medical records, is this kind of thinking old fashioned? Is it acceptable to state that someone should seek treatment where their medical records reside? Even a former president?

Well… yes. Many strident cases are made for “digitizing” medical records through the wounded warrior stories, in which families of injured veterans cart around suitcases of medical records from doctor to doctor, seeking treatment and answers. This is one of the business cases that drives the Nationwide Health Information Network (NHIN), which seeks to provide the trust fabric for secure electronic health information exchange. One of the promises of the NHIN is that you can leave your folder/binder/suitcase at home, because Dr. Smith can obtain the test results taken by Dr. Joshi. It's a fantastic vision of a primary benefit of electronic health records.

I work with the wonderful people behind the NHIN; I work to create the testing and validation processes that will ensure that the systems exchanging health information across this network are capable of doing so. I’ll write more about the work being done, but I work on the NHIN and had to be my own personal NHIN at my doctor’s office last week – Dr. S---  faxed my test results to me, and the e-fax rendered a pdf on my laptop, which I showed to Dr. P--- in his office. I work on the NHIN and realize we’ve got a long way to go before its promise can be realized – we’ve got a long way to go before it would be considered absurd that Bill Clinton would get treatment at a hospital just because his medical records were there.

Why aren’t we there yet? Government, and businesses big and small, are attempting to clear the path to make the sharing of health information simpler – everyone from Dell to seemingly Pizza Hut is getting into the effort. We’d like to hear your thoughts on the largest challenges – time, money, technical hurdles, privacy concerns, workflow modifications, access consent, human nature? – how will conditions unfold so that Bill Clinton can access his medical records anywhere? What will that look like – will Clinton own his information (in a chip in his arm, in his iPhone, in HealthVault or Google Health et al, or in his suitcase full of medical records), or will the data reside where it originated, shareable with others? Is our first step defining standards for machines to exchange data, or defining up a way for people to share information? We’re heading to the Health Information Management Systems Society conference (HIMSS) next week and will report on our conversations, musings, and discoveries. In the meantime, please share your own comments and ideas.
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