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Next-Gen Users Move to ‘Real’ Projects At AGBT as New Systems Make Debut

Existing next-gen sequencing platforms have moved beyond the initial testing phase of applications, and are now being used for a variety of scientific projects, including genome-wide structural variation studies, transcription or methylation analyses, and targeted resequencing, according to platform users.
These users presented their work at last week’s Advances in Genome Biology and Technology Conference on Marco Island, Fla., where two companies also showed new sequencing technologies: Pacific Biosciences and Danaher Motion – Dover.
PacBio presented its third-generation single-molecule, real-time sequencing technology in public for the first time (see related article, in this issue), and preceded its plenary talk with a panel discussion on human genome sequencing and beach fireworks.
Meantime, Danaher Motion – Dover kept its debut comparatively modest by showing small groups of visitors its low-cost open-source Polonator sequencer, which it has been developing with George Church’s group at Harvard (see In Sequence 2/4/2008). It was also the first time the company publicly showcased the instrument.
In testimony to the fact that large-scale sequencing is making a comeback after a slump following the Human Genome Project, the meeting itself reached record attendance this year with 575 registered participants, up from about 400 last year, and about 250 would-be attendees who were turned away for lack of space, according to conference organizers.
While at last year’s meeting, mostly large genome centers and instrument vendors reported results obtained with 454’s Genome Sequencer and Ilumina’s Genome Analyzer, and initial data from Applied Biosystems’ SOLiD system (see In Sequence 2/13/2007), this year, users from many institutions presented scientific projects that involved the use of the new technologies, especially Illumina’s and 454’s, which have been in users’ hands the longest.
“At this meeting, there was just a whole bunch of people successfully using these instruments to learn about biology,” Dick McCombie, a professor at Cold Spring Harbor Laboratory, told In Sequence. “I thought that was really fun to see.”
He likened the transition to the early days of automated fluorescent sequencing. “For the first year or two, you start hearing, ‘Well, this is how we are going to do this,’ and all of a sudden, you start seeing results,” he said.

“The plenary speakers are no longer focusing on the instruments and applications but on the real genome-wide experiments that are being done with these platforms.”

As an example, Joe Ecker from the Salk Institute, in his keynote lecture, talked about the use of “now-generation” sequencing technologies — in his case, Illumina’s Genome Analyzer — to shotgun-sequence bisulfite-converted genomic DNA from Arabidopsis for methylation analysis. During a conference workshop by 454 and Roche, he also presented a collaboration with 454 to sequence an Arabidopsis strain, using 454’s new extra-long XLR reads and long paired-end reads.
Richard Durbin, who also gave a keynote lecture at the meeting, focused on the 1,000 Genomes Project, a collaboration between the Wellcome Trust Sanger Institute, the US National Institutes of Health, and the Beijing Genomics Institute (see In Sequence 1/22/2008). As a pilot project, he and his colleagues sequenced a human X chromosome in collaboration with Illumina, using both single and paired-end reads from the Genome Analyzer.
As an example of the use of ABI’s SOLiD sequencer, Sean Grimmond from the University of Queensland in Australia showed sequence tag data from embryonic stem cell RNA libraries that were generated on the SOLiD system in order to find not only known but also novel transcription activity.
“The plenary speakers are no longer focusing on the instruments and applications but on the real genome-wide experiments that are being done with these platforms,” Elaine Mardis, co-chair of the meeting and co-director of the Genome Sequencing Center at Washington University School of Medicine, told In Sequence by e-mail. “It’s very exciting to see that transition from only a year ago, and means that next year, we will predominate both plenary and concurrent sessions with similar types of talks.”
Several talks in the concurrent sessions, as well as conference workshops organized by Roche/454, Illumina, and Applied Biosystems, focused on new technologies for the sequencing platforms, as well as upcoming improvements to the systems’ hardware, software, and chemistry (see next week’s issue of In Sequence).
Helicos BioSciences showed data from a project in collaboration with Victor Ambros at the University of Massachusetts Medical School to sequence human miRNA for tag counting, as well as data from a BAC sequencing project that involved two-pass sequencing on the HeliScope.
A number of presentations focused on DNA capture technologies, to be used as a front end to different sequencing platforms. These either use microarrays from NimbleGen or oligonucleotides provided by Agilent.
Notably, the meeting devoted an entire concurrent session to bioinformatics, many featuring new tools that help assess the quality of and assemble data from new sequencing technologies.
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