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After a Decade, JGI Retires the Last of Its Sanger Sequencers

By Alex Philippidis

NEW YORK (GenomeWeb News) – The US Department of Energy Joint Genome Institute has retired its last Sanger sequencers after a decade of service, leaving it entirely with next-generation machines.

A ceremony held recently at JGI's Walnut Creek, Calif., headquarters marked the final phase-out of the Sanger line of sequencers, which at their peak consisted of about 84 Applied Biosystems 3730xl machines and 21 GE Healthcare MegaBace4500s running 24/7. The machines generated on average each month about 3 billion bases — the equivalent, according to JGI, of a human genome's worth of plant and microbial DNA sequence data.

As a key center for the Human Genome project, JGI used Sanger equipment in collaboration with colleagues at the Stanford Human Genome Center to decode the sequence of human chromosomes 5, 16, and 19, constituting 11 percent of the total human genome, David Gilbert, a spokesman for the institute, told GenomeWeb Daily News. The chromosome sequences were first published in the journal Nature in 2004.

JGI also applied Sanger sequencing to the genomes of the puffer fish fugu; the sea squirt; and the first tree — a black cottonwood/poplar appearing on the cover of Science in September 2006 — as well as many other plants, microbes, fungi, and metagenomes, Gilbert said.

The institute began running non-Sanger sequencers in 2007, when it shut down the MegaBace line and enabled JGI to free up resources to bring in Roche 454's Genome Sequencer, JGI stated in its 2008 Progress Report.

During 2008, JGI scaled back to 57 ABI 3730xls on the Sanger line, while optimizing and expanding its 454 line, and introducing the Illumina Genome Analyzer into production. Last year, JGI cut its Sanger line further to 15 ABI 3730 capillary, while it had eight Roche 454 systems and seven Illumina systems at Walnut Creek.

JGI had been using the Sanger sequencers for de novo genome sequencing, but that is now handled through the institute's current mix of equipment at its headquarters — eight Roche 454 FLX-Titanium analyzers; 12 Illumina GAIIx analyzers; and two Illumina HiSeq 2000 analyzers, with three more to arrive by month's end, for a total of five.

In addition, JGI is in "acceptance" of a single-molecule real-time sequencer made by Pacific Biosciences. The institute is one of 10 early-access customers identified earlier this year as having agreed to order, at the full list price of $695,000, the SMRT sequencer, PacBio's first commercial sequencer.

"With these new sequencers incorporated into the production line over the last two years, our productivity has risen to 1 terabase in FY09; 5 Tb in FY10 and to a projected over 25 Tb in FY11. To put this in perspective, our total commitment to DOE in FY98 was 20 megabases, which we do now in a few minutes," Gilbert told GWDN.

Researchers at the Lawrence Berkeley National Laboratories — one of six partner institutions whose genomic capabilities are coordinated through the institute — get first dibs on the used Sanger sequencing instruments, followed by the University of California, then the Department of Energy, then the general public.

"There are current negotiations about trading the equipment in question in for some newer instruments," Gilbert added.

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