Applied Biosystems' release of more than 400,000 PCR primer-pair designs and 65 million sequencing reads into the public domain and onto the website of the US National Center for Biotechnology Information could benefit pharmacogenomics research.
The primer sets correspond to exons in about 16,000 human genes, while the 65 million sequence traces come from human, mouse, and rat genomes, the company said in two statements this week. Although ABI is certainly motivated partly by an opportunity to promote its products, the data and designs should prove quite useful to researchers. The primers will fill a near vacuum, since there is apparently no comparable public resource, and they should remove a significant obstacle to resequencing studies. Both releases will probably increase ABI's visibility and the total amount of DNA sequencing going on, which is not a bad thing for the sequencing-tools giant.
The Primer Sets
The 400,000 PCR primer sets, which are intended for use in resequencing, will be available through a new NCBI "Probe Database" on the institute's web site.
The collection of resequencing primers is the result of Celera's huge SNP-discovery effort, said Kevin Corcoran, general manager and vice president of genetic analysis at ABI. "As we go out and talk to everybody, what you hear a lot is that the bottleneck is in designing primers," he said. "There is a great advantage in letting them get on with their work," he added.
"You can literally spend a week or two validating primer sets before you even begin your experiment, and you're going to go through all the time and reagents to validate these before you have a workable primer pair."
The release of the primers may also indicate larger changes afoot in the market. "What we're seeing is a real shift toward resequencing, and this will help in that shift from de novo [sequencing] to resequencing," said Corcoran.
The Atlantic Genetics and Genomics Initiative, a Genome Canada human-gene sequencing project at the Genome Atlantic DNA sequencing facility, will probably use the primers, now that their designs are available in the public domain, Sharen Bowman, the facility's chief technology officer, told Pharmacogenomics Reporter. ABI representatives came to Genome Atlantic last week to publicize the designs' release, she said.
"It will make the computational side of resequencing much easier if there are sets of pre-tested primers out there," said Bowman. Up to this point, the facility had been doing its own primer design for resequencing, she said. "In our hands, about 20 percent of primers that you design actually fail, so you have to redesign or you have to do quite a bit of work to test out what conditions to use for the PCR."
However, Bowman added, "It is kind of an unknown quantity, because they've just been released, and we haven't had a chance to try them and see if they're as good as [ABI says] they are."
Approximately 80,000 of the sets were validated during the Celera SNP Discovery Project, said Abizar Lakdawalla, ABI product manager of resequencing technologies.
ABI is not going to turn any customers away, of course. "If researchers want to come to ABI to have these particular probes made, that's something we'd be very happy to do," although researchers can use the designs freely, Corcoran said.
Bowman estimated that, at best, pre-designed primer sets might save effort and funds equivalent to one full-time salaried lab worker.
"You can literally spend a week or two validating primer sets before you even begin your experiment, and you're going to go through all the time and reagents to validate these before you have a workable primer pair … that's where you're going to save money," said Kevin Knutson, director of the DNA Facility at the University of Iowa.
Although Knutson said he wouldn't characterize primer design as the major bottleneck in a resequencing project informatics weigh heavily good primer design would be of some help, he said.
Ultimately, the availability of useful primers could also allow for easier validation of published mutations, said John Carpten, a senior investigator and director of the Genetic Basis of Human Disease Division at the Translational Genomics Research Institute, in an e-mail exchange.
The primer sets are a "unique resource," said Carpten. "Most research groups rely on in-house primer design and optimization, which slows the discovery process," he said. The availability of the primer designs could allow researchers working on similar projects to adopt a "standard set of primers for specific gene families, such as the kinase genes, which could be used by multiple groups. This would standardize amplification conditions across multiple institutions, allowing for better data integration across labs," Carpten added.
Other primer designs available publicly generally come from primary publications, said Lakdawalla, the ABI resequencing product manager. "For the hot genes, I think there's available primer data, but for the genes that are gaining more relevance now, there may not be that much published data," he said. "I think this is the first time in the public domain that there's a human genome-wide public release," Lakdawalla added.
"I think what you will see is some of the larger academic institutions probably releasing primer sets as well," Corcoran said.
"A significant proportion of the variant-seeker sets are used by commercial institutions" in Europe, such as pharmaceutical companies, whereas in the United States "it's more academic and basic research," said Lakdawalla. Neurology-related primers, metabolic disorder-related primers, and cancer-related primers, particularly BRCA primers, are popular among commercial institutions, he said.
Lakdawalla characterized the primer-design release as partly altruistic. "We have more data than we have products there's no way we can make products for the whole genome it's hard to predict demand," but the company also has products tied to many genes, he said.
The human, mouse, and rat genome sequence traces hail from the sequencing efforts of ABI's sister company Celera Genomics. ABI has also donated 7 million human and mouse SNPs to NCBI's SNP database, the firm said. The sequence data added to GenBank is hyperlinked to relevant ready-to-order microarrays and TaqMan assays, ABI said, making good on two goals ABI set for itself to release its genome data into the public domain, and to build a stronger web presence.
In May, Celera Genomics called it quits on its commercial genome database, vowing to "substantially discontinue" the offering after the June 30 expiration of most customer subscriptions. The company said it would make its data public through the National Center for Biotechnology Information after July 1.
"Right now, the focus is [on] 'How do we provide an advantage for AB's customers basically [in] using AB's instruments and reagents and other products [and] how do we help them with their data workflow?' And really that's independent of having any proprietary data," Tony Kerlavage, senior director of ABI's online information business, told Pharmacogenomics Reporter's sister publication, BioInform, in May.
Kerlavage told BioInform that ABI's web presence is "evolving, and we are going through a lot of focus to make the purchasing of these information-rich products, and other products in general, easier for our customers. So we are putting a major effort into our portal and into our e-commerce system to enhance that purchasing experience."
Chris Womack ([email protected])