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ABRF Survey Aims to Shed Light on Second-Gen Sequencing in Labs


Members of the Association of Biomolecular Resource Facilities are currently assessing how core facilities and other laboratories around the world are adopting second-generation sequencing technologies.

Several weeks ago, the organization's DNA Sequencing Research Group posted its first survey on second-generation sequencing technologies, asking laboratories about their use of the new platforms. Results from the survey, which is open until the end of this week and can be taken online by any laboratory, will be presented at the ABRF's annual meeting in Memphis, Tenn., next month.

The need for a survey on the new sequencing platforms became apparent to DSRG members at last year's ABRF meeting, where "there was quite a bit of buzz about next-gen sequencing," recalled Peter Schweitzer, director of the DNA sequencing and genotyping lab at Cornell University and chairman of the DSRG. "At that time, we did not have any information [on] what labs were thinking about" the new technologies.

Anecdotally, he and his colleagues knew that core facilities were starting to adopt the new platforms, but no hard data was available, so this year, "we thought we would try to get a handle on where core facilities are in terms of these new next-generation sequencers," he said.

"Our survey is probably not going to answer that question, but at least give an idea," he said. "We just don't know how pervasive these things are yet, so we just wanted to try and get a snapshot of where the field is right now."

The survey addresses a variety of topics, including how many and what type of second-gen sequencer a laboratory operates, where the funding for the instrument came from, what the main applications are, what types of data analyses a lab provides, what software they use, what concerns users have about the technologies, and what types of additional platforms they are considering.

Part of the survey covers Sanger sequencing, as some labs still primarily use that technology, according to Schweitzer.

Five of the eight current members of the DSRG currently own second-generation platforms, he said, including his own lab, which has two Illumina Genome Analyzers II and one 454 GS FLX.

According to its website, the ABRF represents more than 250 core laboratories in government, academia, research, industry, and commercial settings and has nearly 1,000 individual members.

Grown out of the Protein Society, the association has traditionally focused more on proteomics, though about a third of the membership is interested in genomics, primarily DNA sequencing, according to Schweitzer.

The ABRF Yellow Pages, which lists academic and for-profit laboratories that offer commercial analytical services, has 43 entries for DNA sequencing services, of which 36 are located in the US.

The latest survey is not the first the DSRG has been conducting: In 2006, it presented the results of a "General Survey of DNA Sequencing Facilities," in which 61 laboratories participated, after similar surveys in 2003 and 2000. These surveys focused on Sanger sequencing, but "we really did not want to do simply another Sanger sequencing survey, because Sanger sequencing has pretty much stabilized in terms of developments," Schweitzer said.

As of last week, almost 40 laboratories had taken the latest survey, which can be accessed here.

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