Baylor College of Medicine’s Human Genome Sequencing Center is increasing its fleet of 454 Genome Sequencer FLX instruments to 10 from three by year’s end, 454’s parent Roche said this week.
Stocking up on the instruments is “laying down the pathway” for large-scale resequencing projects “in the anticipation that the unreserved support [from funding agencies] will come for it,” according to Richard Gibbs, director of Baylor’s Human Genome Sequencing Center.
“We have been holding back on the different technologies, deciding which one is going to have the biggest impact in the near term, and this is our statement here,” Gibbs told In Sequence this week.
Besides 454 machines and traditional Sanger sequencers, Baylor owns one Illumina Genome Analyzer and recently installed one Applied Biosystems SOLiD sequencer.
Baylor decided to invest heavily in 454’s technology after its recent development of a capture technology that allows users to selectively amplify large numbers of DNA targets for sequencing on a next-generation system. “That application and the potential for that application, that was the dealmaker,” Gibbs said.
Gibbs, who until March was a member of 454’s scientific advisory board, developed the method with his Baylor colleagues in collaboration with NimbleGen Systems, also a Roche subsidiary. In the study, they selected almost 6,500 human exons on the arrays and used the 454 sequencers to analyze them.
Details of the method were published earlier this month in Nature Methods alongside two other publications on other DNA capture methods (see In Sequence 10/16/2007).
NimbleGen has since developed a series of arrays that capture all human exons, 454 reported at a conference earlier this month. According to Gibbs, the arrays go hand in hand with 454’s technology. 454’s long reads “very well match exon reads” and are “perfect for mutation detection” because the technology is “exquisitely sensitive to changes in the normal patterns,” he said.
On the other hand, “we have not demonstrated success with the capture [method] and the [Illumina] combination,” Gibbs said, adding that this mix might still work well “for some applications.”
But exon sequencing is not the only application that Baylor has in mind for its FLX stable. For example, the scientists also plan to harness the sequencers for microbial sequencing under the Human Microbiome project, which is part of the NIH Roadmap program (see In Sequence 6/19/2007). “We know [the instruments] are performing extremely well in the microbial world,” Gibbs said.
Also, they want to use the technology to “upgrade” mammalian genomes by creating additional-fold coverage for those genomes that have only been sequenced to a limited extent.
Long reads are among the main boons of the technology, according to Gibbs. “It’s easier to map the reads in the resequencing applications,” he said. “That’s been the bugbear of the other [platforms].”
Even the higher cost of sequencing on 454’s platform does not make a difference. “The higher per-base cost of the raw 454 sequences are outweighed by the higher utility of the data, primarily from the better mapping that comes from longer reads lengths,” Gibbs said.
What would change the picture is if short-read high-throughput platforms like those from ABI or Illumina were to develop 50-base paired-end reads, he said. “Extremely low cost and 50 bases on each end ― that would be a different equation.”
ABI’s SOLiD currently offers paired ends with 25-base reads, and Illumina has been developing pairs with 36-base reads.
In the meantime, Baylor will be an early-access user for upgrades to 454’s FLX, which will include an increase in read lengths beyond 400 bases and in throughput to one gigabase per day, along with reduced cost per base (see In Sequence 10/9/2007). “We are confident that the 454 group will deliver these 500-base reads ... and we have seen other performance elements that are also extremely encouraging,” Gibbs said.
But the decision to go with 454 does not mean this platform is the best solution for every application. For example, Gibbs acknowledged that “beautiful studies” have been published that used Illumina’s Genome Analyzer for ChIP-sequencing.
However, “in the real world, you have to make some predictions, and you have to step up and make a selection early,” he said. “It’s a moving field, and that’s our statement right now.”
Baylor’s is not the only large-scale genome center to build a stable of next-gen sequencers of the same type: The center’s investment comes several months after the Broad Institute installed at least 16 Illumina Genome Analyzers (see In Sequence 7/31/2007).