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At Marco Island, Next-Gen Sequencers Reach Milestone as Outside Researchers Show Data

Next-generation sequencing reached a milestone last week when for the first time, independent researchers presented data that was generated on the platforms of all three front-runners for a variety of applications.
Presentations at the Advances in Genome Biology & Technology Conference, held at Marco Island, Fla., last week, showed sequencing data generated by instruments made by 454 Life Sciences, Illumina (formerly Solexa), and Applied Biosystems for applications ranging from whole-genome sequencing to genotyping and transcriptome analysis.
And as next-gen sequencers become more robust, interest in them continues to grow. Several meeting participants representing independent research institutes, university departments, or biotech companies with DNA sequencing core facilities told In Sequence that they had committed to install one of the three platforms in-house within a year, or were planning to adopt next-generation sequencing in the next several years.
They said they hoped that information presented at Marco Island might help them decide which instrument to buy.
Responding to demand for more and independent information about the new instruments, conference organizers held a tutorial workshop ahead of the meeting on the “utilization of new DNA sequencing technologies.”
The standing-room-only workshop, attended by at least 140 participants, included tips from researchers at the Broad Institute on what to consider before investing in a next-generation sequencer (see related article in this issue), a report by a small university core facility that recently acquired a 454 sequencer; and a comparison between all three platforms by a scientist from the Wellcome Trust Sanger Institute (to be covered in more detail in upcoming issues of In Sequence).
The enthusiasm for next-generation sequencing was also reflected in the overall conference attendance. This year’s meeting had about 400 registered participants, a number the annual event had not reached since 2002, according to Eric Green, scientific director of the NHGRI and co-chair of the meeting. He attributed this number to an increasing interest in the “nature of the science” presented at the meeting, in no small part fueled by the new technologies.
New sequencing technologies are finding “a growing base” and a “wider array of applications, not only at the large-scale genome centers,” Green said during his introduction to the meeting.
Two of five plenary sessions were devoted to the development and applications of DNA sequencing technologies “en route to the $1,000 genome,” while two additional sessions with parallel tracks covered “DNA sequencing technologies.” Many of these featured back-to-back presentations by users or developers of the 454, ABI, or Illumina platforms.
The talks covered a variety of applications and new developments of the three technologies. Several of the presentations came from representatives of the three large-scale genome centers, which have had the most time to study 454’s and Solexa’s platforms in-house (see upcoming issues of In Sequence for more detailed coverage).  
For instance, both the Broad Institute and the Baylor College of Medicine Human Genome Sequencing Center reported using 454’s platform to sequence dozens of organisms, mostly microbes with relatively small genomes.
Baylor’s team is also involved in a collaboration with 454 to sequence James Watson’s genome. The company plans to make the data publicly available in the future once it has reached a high-quality assembly and ironed out some remaining ethical issues.
Further, researchers from the Genome Sequencing Center at the Washington University School of Medicine and from the Broad Institute reported their initial experience with Illumina’s Genome Analyzer, which included detecting SNPs in bacteria and performing whole-genome sequencing on microbes. The Broad researchers also presented new software that will allow them to assemble genomes from 30-base “microreads,” similar in length to data from Illumina’s and ABI’s new platforms.
Researchers at Agencourt Bioscience, a unit of Beckman Coulter, used ABI’s Sequencing by Oligonucleotide Ligation and Detection, or SOLiD, technology to sequence mutants of P. stipitis, a xylose-fermenting yeast, and scientists at Stanford sent samples to ABI for SOLiD sequencing to characterize the positioning of nucleosomes in the C. elegans genome.
The three companies also presented updates on their technologies, including talks by Illumina and ABI on their strategies for creating paired-end reads that will allow them to map even short reads unambiguously to a genome. Paired reads, which 454 introduced last year, open the door to de novo assemblies, sequencing through repeat regions, and characterizing deletions and insertions in a genome, for instance.
Meantime, a handful of talks covered other next-gen platforms that are in the works, some of which are expected to reach the market this year: Helicos BioSciences, for example, gave an update on its single-molecule sequencing technology, which it said will reach beta testers by the end of this year (see related article in this issue [LINK]). Also, Jingyue Ju, head of DNA sequencing and chemical biology at the Columbia University Genome Center, introduced his four-color SBS-on-chip technology that Intelligent Bio-Systems plans to commercialize this year (see GenomeWeb Daily News 12/12/2006).

New sequencing technologies are finding “a growing base” and a “wider array of applications, not only at the large-scale genome centers.”

‘Keep Us On Our Toes.’
Although the meeting did not have an exhibition venue for companies, the presence of the three current next-generation sequencing vendors was hard to escape, and their competition tangible.
“These guys will keep us on our toes,” said Michael Egholm, vice president of molecular biology at 454, referring to ABI and Illumina — but before pointing out that it was his company’s instrument that made it onto the January cover of Nucleic Acids Research relating to the 30th anniversary of Sanger sequencing.
Not to be outdone, ABI had hotel room key-cards, as well as conference backpacks, emblazoned with an ad for its SOLiD technology.
ABI, Roche/454 Life Sciences, and Illumina also all held separate presentations during conference lunch breaks, during which they featured their own scientists as well as outside users of their sequencing platforms. A researcher at Myriad Genetics in Roche’s workshop, for example, presented an assessment of the 454 technology for diagnostic sequencing.
And ABI, which is behind 454 and Illumina in bringing a next-generation sequencer to market, had a prototype of its SOLiD sequencer on display in a conference hotel suite, where it showed off the instrument to small groups of participants.
While second-generation DNA sequencing was well represented at the meeting, third-generation technologies received short shrift, presumably because they are not yet ready for prime-time.
For example, only a couple of presentations covered advances in nanopore technology, believed by many to be an important component to lead the way to the $1,000 genome.
Also, neither VisiGen Biotechnologies nor Eagle Research and Development — third-generation sequencing companies in which ABI has invested over the last two years — gave presentations at the meeting.
However, many third-generation technologies made appearances at a closed gathering of NHGRI Advanced Sequencing Technology awardees (see table in last week’s In Sequence) that preceded the conference.
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