As next-generation sequencing technologies are becoming part of routine production sequencing, sequencing centers have begun retiring some of their high-throughput capillary electrophoresis Sanger instruments, In Sequence has learned.
Several large genome centers in the US and the UK confirmed that they have started to shrink their Sanger capacity. Also, used equipment vendors are noticing that sales of used 3730xl DNA Analyzers — ABI’s 96-capillary sequencer, the workhorse of the large genome centers — have been growing since mid-2007.
For instance, one such vendor, Azco BioSystems, has bought or sold two 3730xls in 2005, five units in 2006, but 28 units last year and more than 50 units so far this year, the company’s president, George Yang, told In Sequence last week. He did not provide specifics on the origins of these systems because of confidentiality agreements with customers.
Citing anecdotal market observations, Yang said that “the market is flooded” with 3730xls. His company sells new and refurbished instruments for DNA sequencing, PCR and RT-PCR, HPLC, and mass spectrometry. Azco also offers maintenance services for DNA sequencers and RT-PCR machines, and has been servicing 3730xl instruments at several genome centers and major university labs.
“There is a huge increase in [used 3730s]” said Chris McManemin, whose company, Scientific Asset Management, buys and sells large laboratory equipment. McManemin, who also cited anecdotal evidence, estimated that each of the large US genome centers is “easily releasing 25 to 40 of them.”
For comparison, as of last August, the Broad Institute had more than 100 ABI 3730s (see In Sequence 9/4/2007). Similar numbers were not immediately available for the other genome centers.
“What seems to be happening is that the people who have many 3730s are keeping a certain percentage of them,” said Mike Sherrell, owner of Grizzly Analytical, a dealer of used and reconditioned biotech laboratory equipment.
Sherrell said his shop currently has “at least” 30 ABI 3730xls available for sale. For core facilities and other labs wanting to increase their Sanger sequencing capacity, now might be a good time to buy: Grizzly advertises the instruments on its website for $95,000, “installed and warranteed” and “complete with all necessary software and accessories.”
That price is a 74-percent drop from the $365,000 that ABI charged for the 3730xl as of mid-2006 (see In Sequence 9/18/2006). At the end of 2007, the instruments were still selling for between $130,000 and $150,000 on the used-equipment market, according to McManemin.
Sherrell said that he has sold about 10 units since the fall of 2007. Before next-generation sequencers came out, he said, 3730s “were very, very rare on the used market.”
Part of the reason, he said, is that the 3730 is “an extremely robust, efficient machine” and “people that use them were very happy with them.”
Buyers of the used instruments consist of universities and companies both in the US and abroad, including an oligonucleotide manufacturer and a personal genomics service provider. “In the long run, it’s going to be mostly universities,” according to Sherrell. Approximately five instruments went to China, he said.
Several genome centers confirmed that they are indeed starting to replace some of their high-throughput Sanger sequencers with next-gen technology.
For instance, the Wellcome Trust Sanger Institute started retiring ABI 3730s in late 2007. As of next week, the institute will have 45 instruments remaining, down from 75 before it began to bring in new sequencing technologies.
“We don’t plan to decommission any more until late 2009 as we have large-scale projects already committed requiring ABI3730s,” said Carol Churcher, who heads the institute’s sequencing operations. As of late January, the Sanger Institute had 27 Illumina Genome Analyzers, three ABI SOLiD sequencers, and two 454 Genome Sequencers (see In Sequence 2/5/2008).
Prior to next-generation sequencers, 3730s “were very, very rare on the used market.”
Sanger sequencing is also declining at the J. Craig Venter Institute. “Yes, we are moving to replace the ABI 3730xls, although they still have utility for some sequencing projects in the near term,” Yu-Hui Rogers, scientific director of the institute’s Joint Technology Center, told In Sequence by e-mail.
“Since we've opened the JTC, an important component of our facility has been the new sequencing technology testing lab,” she said, “the hope being that new technologies would come along to replace the last generation.”
Platforms the institute has evaluated and uses include 454’s Genome Sequencer, ABI’s SOLiD, and Illumina’s Genome Analyzer, she said. Rogers, who is also the JTC’s director of new technology development, did not mention how many 3730xls the institute has decommissioned, and how many it currently operates.
The Joint Genome Institute’s production genomics facility retired its 36 MegaBace 4500 high-throughput Sanger sequencers in August 2007, according to an institute spokesman, but has no immediate plans to decommission any of its more than 70 ABI 3730xls.
The institute decided to phase out the MegaBace platform, which it had been using for the last eight years, “to allow for the integration of next-generation technologies,” which currently comprise two 454 Genome Sequencers and two Illumina Genome Analyzers, he said. However, he added, “we are still heavily invested in Sanger sequencing, particularly for big assemblies and metagenomes.”
That is true for others as well. “We have not yet decreased our 3730xl capacity, as there are projects ongoing at our center that are best performed on this platform,” said Marco Marra, director of the Genome Sciences Center at the British Columbia Cancer Agency, in an e-mail. He did not mention how many instruments the GSC owns.
At least one sequencing facility has decided to forgo Sanger sequencers altogether: The Ontario Institute for Cancer Research, which recently installed five Illumina Genome Analyzers and five ABI SOLiD systems in its brand-new sequencing facility, is outsourcing its Sanger needs, which will mostly comprise validation sequencing projects (see In Sequence 3/18/2008).
It is unclear how the recent increase in used 3730s will affect ABI’s future instrument or consumables sales, but the company says it is prepared. “With the emergence of next-generation sequencing in the life sciences arena, Applied Biosystems anticipated and planned for the evolving needs of our customers, including large genome centers,” a company spokesman told In Sequence by e-mail. “The transition is proceeding as expected, including the anticipated decommissioning of some capillary electrophoresis genetic analyzers.” The list price of the 3730xl remains unchanged, he said.
During a January quarterly earnings call, ABI President and COO Mark Stevenson said that “[capillary electrophoresis] instrument placements are declining in the research market as instrument funding shifts towards next-generation sequencing platforms” and that “related CE consumable volumes continued strong.”
3730s, he added, were “already a fairly small portion [of instrument sales] since they were mainly [geared towards] the high-throughput customers.”
Applera CEO Tony White said during the call that even though some customers are “decommissioning some of their CE-based systems, they continue to use CE for many of the different applications.”
The Broad Institute, Baylor College of Medicine’s Human Genome Sequencing Center, and Washington University School of Medicine’s Genome Sequencing Center did not return phone calls and e-mail requests for information and comment.