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"Rapid protocol standardization is important and a major advantage of the Illumina platform."
Charles Nicolet, Ph.D.
Director of the DNA Technologies and Expression Analysis Cores, University of California, Davis
An early adopter of Illumina technology, the UC Davis DNA Technologies and Expression Analysis cores started with high-throughput genotyping on the BeadArray Reader in 2005 and now support arrays, gene expression, and sequencing for a thriving community of researchers working on wildly diverse genomic projects- from pine trees to lettuce pathogen resistance to the origin of domestication in cats.
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Q&A with Dr. Charles Nicolet
What kind of projects come through the UC Davis core lab?
At UC Davis, much of the research is not focused on human or mouse. The GoldenGate technology is very approachable and a good entry point for people working on different organisms. Since many of the GoldenGate Assay reagents are generic, people can order their species-specific oligo pool (the OPA) and plug in to off-the-shelf Illumina reagents. As a result we started doing these really interesting genotyping projects on all kinds of organisms.
One of our very first projects was a pine genotyping project with David Neale. Early on we also got into studying pathogen resistance of lettuce with the Michelmore lab. We’ve done an armadillo project. We did an interesting genotyping project with Leslie Lyons looking at the origin of domestication in cats.
We have found Illumina genotyping to be very flexible, the tools are there and the assays are proven to work in all kinds of systems. As long as researchers have SNPs or sequence data, they can use Illumina technology. For our customers, there is always some reluctance around the upfront costs to get the oligonucleotides synthesized. But once we started giving people back their data, they realized that the quality of the genotype calls was so good and the numbers of SNPs they were getting were so large that they were able to complete mapping projects in just a fraction of the time it previously took.
With the investigators at Davis leading the way, we believe we were one of the first core facilities to take on genomic projects on many different organisms.
In addition to the BeadArray Reader, what other technologies and services do you provide?
We started running gene expression chips soon after acquiring our Bead Array reader, which was convenient because the same instrument used in genotyping could be used for a whole other set of experiments. We also purchased the BeadXpress several years ago because we were very interested in its ability to do smaller numbers of SNPs at a great price point.
By early 2007, all of a sudden everyone had to have a next-gen sequencer, so we began to evaluate all the platforms. Rapid protocol standardization is important and a major advantage of the Illumina platform. As a core lab, you know you’re going to get all kinds of samples and you just don’t have time to do a lot of R&D to get things working from scratch. Illumina really helped out our workflow by having kits for sequencing applications. The mRNA-Seq Kit really took off for us, as well as the microRNA Kit. Things like that really do lower the barrier to entry because the kits are straightforward and they work. In general we felt really comfortable working with Illumina. We knew they had good tech support, and they were dedicated. That helped a lot when we were making our decision on whom to partner with for next-generation sequencing.
How do you see sequencing and arrays working together?
Sequencing and arrays are working well together in our facility. People analyze their model organisms with high-throughput sequencing and find hundreds, if not thousands, of SNPs fairly readily. It’s a bonanza. And then they’ll move those into GoldenGate or Infinium assays. I talked to one researcher who was going to do a 1,000 SNP GoldenGate but they got so many SNPs from the sequencing that they did with us, they just decided to scale that up to an Infinium, to ~10,000 SNPs on iSelect.
What direction do you see projects at the UC Davis core facilities going in the next couple of years?
I see us doing a lot of whole genomes, projects that I think we’ve just started thinking about how to approach. Lots of microbial and metagenomic work. I’ve talked to a person who wants to sequence the genome of the vanilla bean tree. I see a lot more genetic studies involving de novo sequencing of organisms that we’ve been genotyping: mosquito, salamander, red fox, Drosophila. I think it will be really fun to characterize all these organisms, and the cost is getting very approachable.
Researcher Bio
An early adopter of Illumina technology, the UC Davis DNA Technologies and Expression Analysis cores started with high-throughput genotyping on the BeadArray Reader in 2005 and now support arrays, gene expression, and sequencing for a thriving community of researchers working on wildly diverse genomic projects- from pine trees to lettuce pathogen resistance to the origin of domestication in cats.
At Illumina, our goal is to apply innovative technologies and revolutionary assays to the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. These studies will help make the realization of personalized medicine possible. With such rapid advances in technology taking place, it is mission critical to have solutions that are not only innovative, but flexible, scalable, and complete with industry-leading support and service. As a global company that places high value on collaborative interactions, rapid delivery of solutions, and prioritizing the needs of its customers, we strive to meet this challenge. Illumina's innovative, array-based solutions for DNA, RNA, and protein analysis serve as tools for disease research, drug development, and the development of molecular tests in the clinic.