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Rockefeller s Zhao on the Impact of New High-Density SNP Chips


Name: Connie Zhao

Title: Director, Genomics Resource Center, Rockefeller University

Professional Background: 2004-present, director, Genomics Resource Center, Rockefeller University; 2003-2004, director, Genotyping Resource Center, Rockefeller University; 2002-2003, senior scientist, Tecan; 2000-2002, senior scientist, Motorola Life Sciences Division; 1995-2000, postdoctoral associate, Rockefeller University.

Education: 1995 — PhD, molecular genetics, Albert Einstein College of Medicine; 1988 — MSc, biochemistry, Beijing University, China; 1985 — BS, biology, Beijing University, China.

Last month, Illumina released its Sentrix Human Hap300 Genotyping BeadChip for SNP genotyping experiments, the second of high density SNP chips to hit the market after Affymetrix released its 500K Mapping Array Set in October 2005 (see BAN 1/17/2006, BAN 10/5/2005).

The impact of these new, high-density chips has been evident across the microarray space. But how are medium-sized core facilities that provide genotyping services handling the advent of these new products?

Connie Zhao, director of the Rockefeller University's Genomics Resource Center, has experienced these changes in microarray technology from the perspective of both academia and industry, where she worked at Motorola's Life Science Division for two years when it had its CodeLink business, and at Tecan for one year. She has also held her current position since December 2004 and has overseen the integration of the new genotyping technologies launched over the past few months by Affymetrix and Illumina into the center's offerings.

BioArray News spoke with Zhao this week to discuss these changes.

How did you wind up in your current position?

I did my post-doc at Rockefeller so I know this university very well. Then I worked in the biotech industry for a few years. And, as you know, there have been a lot of changes in biotech companies. And there was an opening in this position and I applied. As for why, I do enjoy working in an academic institute because there are lots of activities.

Rockefeller used to have separate centers for genotyping — where you were the director — and for gene expression until Dec. 2004. Why was the decision made to fuse your Gene Array center and Genotyping centers at that time?

Well one reason is that the director for the Gene Array Resource Center left the university, and, instead of hiring another director, the university decided to merge the two. But the major reason is that these two centers really share a lot of common instruments and technologies. Before, microarrays used to be mostly used for gene expression and the genotyping was mostly done on a microsatellite platform. But since two years ago most SNP genotyping has been done on microarrays, so it really made sense to combine the two.

Do you anticipate any major changes in the near future or are you satisfied with the technology you currently offer?

We constantly introduce new technologies and instruments. The most recent one is the expanded capacity on the Illumina platform, so we will be able to do whole human genotyping on Illumina.

How have the recent launches of the Affy 500K Mapping Array Set and Illumina HumanHap300 arrays impacted your center?

There has been more usage. There are really two ways of looking at it when you are talking about higher demand — there is the number of labs and then the number of samples. We don't really have that many labs because usually a whole human genome genotyping project is big and very expensive.

But in terms of samples, the new chips have definitely increased the usage of the center.

What kind of support have you received from Affymetrix and Illumina with regards to implementing services for these new technologies?

With any new platform or any new product from these companies, application scientists come to give us the full training. That means we run a full assay together. And that's the initial training. Later on, if we have questions or problems we usually contact their technical support for answers. Their application scientists usually come to see how things are going and if we have any questions. So we do get good support from these companies.

It's pretty standard. Usually all of these companies want their products to work well. Their technical support can be accessed at a 1-800 number, you can call them anytime. We are very happy with their support.

Who are your primary users?

Our main purpose is to serve Rockefeller University, but we do have users from other institutes in New York, other states, even other countries.

We cannot provide a service to companies. We do provide a service to other academic institutes, but it has to be a nonprofit effort.

The university provides us with funding and we have a charge-back structure to charge a fee for users.

You mentioned that you used to do a lot of genotyping using a microsatellite platform. You still have that service, but is there the same kind of demand for that service as there was before the new Illumina and Affymetrix chips came out?

There is definitely less of a demand. People used to use microsatellite genotyping for whole-genome scanning, and the SNP arrays — Affymetrix or Illumina arrays — definitely have an advantage over microsatellite genotyping [in that regard]. But people still use our microsatellite genotyping for mouse. So maybe in the future when there are more mouse SNP arrays, that will further reduce the usage of microsatellite genotyping.

Have you ever stopped using a technology altogether due to lack of demand?

Not entirely. Well, we have an in-house microarray printing service too. We can print in-house glass slides. That usage definitely has been going down a lot. Because there's a lot more [content] on the commercial arrays that are available. There are still people that may work with a particularly weird species where there are no commercial arrays available. So there are some people that still use that. But I can imagine that in the future if nobody needs that we'll just close that service.

Where did you work when you were working in the biotech industry?

I was working at Motorola's Life Science Division when they had their microarray business [CodeLink] for two years. Then I worked at Tecan for one year.

How did you find the change of going from academia to industry and back to academia, personally?

Yeah, they are two different worlds, but I have always been in the research field. In the companies I was always in the R&D departments, so it wasn't that dramatic a change in what I do day to day. I do enjoy working in an academic institute more, I think because there are more projects and more activities.

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