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NCGR, Focusing on Sequencing and Support Software, Buys an Illumina Genetic Analyzer

After laying off about a third of its staff two weeks ago amid a funding crunch (see In Sequence 6/19/2007), the National Center for Genome Resources is gearing up its new sequencing facility, which it hopes will land it more projects and help it develop new software.
“Our assessment was that we needed science-driven proposals instead of software-driven proposals, where the software [would be the] support, not be the cornerstone,” said Bill Beavis, the center’s exiting chief scientific officer.
Using a recent $600,000 grant from the state of New Mexico (see In Sequence 9/1/2007), the center just acquired an Illumina Genetic Analyzer, which is expected to be installed this week at its Santa Fe facility. The new sequencing facility is a collaboration with the New Mexico Institute of Mining and Technology.
Greg May, a program leader at NCGR who is in charge of building the sequencing facility, said that NCGR looked at Roche’s 454 FLX, ABI’s SOLiD, and Illumina’s Genetic Analyzer, sending the companies a brain RNA sample to sequence, and testing the data on its new DNA variant analysis software, Alpheus.
“For our needs [with regard to] timeframe and availability, we have chosen the Solexa [sequencer] as our technology platform for our first instrument purchase,” May said, adding that the center might buy a second next-generation sequencer within the next year or so.
All research institutions in the state of New Mexico will have access to the instrument, but NCGR is also in the process of setting up out-of-state and international collaborations, and plans to provide fee-for-service work.
Internally, NCGR is planning to use the instrument for two types of projects: medical resequencing and plant biology or agricultural projects.
The new instrument will help with NCGR’s ongoing collaboration with the Mental Illness and Neuroscience Discovery Institute, another non-profit based in New Mexico, to identify the genetic basis of schizophrenia (see In Sequence sister publication GenomeWeb News, 3/29/2006).
The researchers also want to resequence various crop species, including soybean and maize, at the genome and transcriptome level, as well as resequence a number of model plant species, such as Medicago truncatula, a legume model.
In addition, in collaboration with 454 Life Sciences and an undisclosed partner, NCGR scientists sequenced the transcripts from 12 unspecified cancer tissues samples as well as controls, looking for consistent variants between them. They have submitted their results for publication.
Earlier this year, NCGR said it was seeking $1.1 million in federal funds for the sequencing center, but that appropriation fell through. Instead, the state of New Mexico chipped in another $667,000, bringing the total funding for the new sequencing facility up to about $1.2 million. This will be used to build the lab space and purchase additional equipment, Beavis said.

“Our assessment was that we needed science-driven proposals instead of software-driven proposals, where the software [would be the] support, not be the cornerstone.”

The plan is also to use some of the funding to generate preliminary data for grant applications with “various funding agencies,” according to Beavis, who is leaving NCGR to become a professor of plant genomics in mid-August at Iowa State University, his alma mater.
This way, NCGR, which is mostly funded publicly, hopes to obtain more funding. “For about three years, we really invested heavily in more advanced software engineering,” said Beavis. However, in grant applications, that approach did not compete as well as more prototypic software, he said. “We found that we can get by with more alpha or beta releases instead of full commercial-grade software.”
As a result, the center decided to shift focus to develop early versions of sequencing-related software, “driven by the science questions of interest instead of just the software itself.”
To be sure, about half of NCGR’s remaining staff will still be involved in software development. “That did not go away at all,” Beavis said. In addition to sequencing-related projects, there are still a number of other software projects ongoing, such as the Legume Information System.
One of the first sequencing-related products is Alpheus, a DNA variant detection software. Stephen Kingsmore, NCGR’s president, showcased the product at a sequencing conference in San Diego in March.
Alpheus was built with short reads from next-generation sequencers in mind, which it can accurately place on a reference genome. However, it can handle different types of sequencing data, ranging from Sanger reads to 454, SOLiD, and Illumina.
At the moment, NCGR offers access to Alpheus as a service, but in the future, “we will have to decide how we want to release the source code,” Beavis said.

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