The Genome Sequencing Center at the University of California, Santa Cruz, has recently begun offering sequencing services for researchers at external academic institutions as part of a broader effort to develop improved protocols for next-generation sequencing platforms.
The UCSC center currently has a Life Technologies/Applied Biosystems SOLiD and a Roche/454 FLX Titanium and expects to add an Illumina Genome Analyzer in the future, Elizabeth Mitchell, the coordinator of the center, told In Sequence.
"We constantly want to be expanding and integrating new platforms because our ultimate goal is to offer a center that will allow customers — based on budgetary concerns or experimental design — to choose a platform that's best for what they're tying to do," Mitchell said. "We want to be able to work closely with those researchers to achieve their goals, and also to hopefully design protocols that can overcome problems that maybe don't have an obvious answer."
This collaborative approach — with the ultimate goal of driving new technology advances — should set the UCSC center apart from commercial sequencing service shops, Mitchell said.
"We're really trying to build relationships with our customers here to help them achieve any and all goals that they want," she said. "We're willing to work with researchers — as opposed to just working for them — to come up with new techniques and new experimental designs to help them achieve their goals."
Mitchell declined to provide pricing information for UCSC's sequencing services, noting that the price for a project is determined on a case-by-case basis. She noted, however, that the center plans to charge only for its reagent costs and "university-dictated indirect costs, like overhead."
Nader Pourmand, assistant professor of biomolecular engineering at UCSC and director of the sequencing center, said that the group, which includes nine technical staffers in addition to himself, is looking to collaborate with scientists who "have a challenge that current protocols don't address."
He added that another advantage that the UCSC group offers is its proximity to the UCSC Genome Bioinformatics Group, led by David Haussler. "They are an icon for bioinformatics … and his group and people are useful and available for discussions," he said. "For users, it's a unique opportunity."
Room for Improvement
The UCSC sequencing center offers a range of applications, including whole-genome and targeted sequencing, resequencing, RNA-seq, microRNA and small-RNA sequencing, ChIP-seq, and metagenomics.
Pourmand told In Sequence that his particular focus right now is developing new protocols for single-cell sequencing, since it is difficult to extract DNA or RNA from single cells without losing material. "People are using microfluidics and things, but still you are losing quite a bit of material, so that's a challenge," he said.
"What we are trying to do is develop an assay so that everyone can do that — not just one site with a huge resource."
The group is also investigating ways to improve paired-end sequencing for SOLiD. Namely, Pourmand said they are looking to increase the size of the inserts from a current range of around 6 kilobases to "at least" 30 kilobases.
"This is a challenge that everyone has, but we believe that we have a way to solve it," Pourmand said, without elaborating.
He said that his group has also worked to automate sample preparation across the two platforms it has in-house in order to save time for large sequencing runs with many different samples.
He noted that most investigators are not sequencing large genomes, so they don't require the full capacity of a second-generation sequencer. "People would like to put 50 to 100 different samples in one run, but the bottleneck is laboratory preparation,” he said. “If you do that manually, it's almost impossible. A good technician takes three of four days for a few samples, but preparing 50 samples would take weeks."
Pourmand said that his group expects to soon publish one of its automation protocols that enables a technician to prepare 48 samples in less than a day.
The UCSC center is also looking into ways to improve the efficiency of emulsion PCR and other reagents in order to reduce the total cost for sequencing consumables from a current level of several thousand dollars per run to under $1,000.
"Right now, the efficiency of emulsion PCR, for a good run, is 10 percent. Which means one emulsion PCR run is about $1,500," he said. "We know we can improve it to somewhere between 25 and 35 percent yield of emulsion, so we're already cutting the emulsion costs down to $500 per run, so that's a cost saving right there."
Another area the UCSC team is looking to improve is input material for sequencing experiments. Current platforms require between 1 microgram and 5 micrograms of DNA, he said, while paired-end sequencing can require much more — up to 40 micrograms of DNA in some cases.
"In most cases, that's not feasible, so we're working to improve that to go below 1 microgram for mate pair sequencing," Pourmand said.